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I'm currently learning the how's and why's of bioinformatics, this is the third three I build and I noticed that the more sequences I add, the lower is the bootstrap.
My sequences were trimmed using trimAl I choose to obtain them with no gaps. The evolutionary model was chosen using the Jmodeltest software and the phylogenetic tree was generated on Mega.
This is a Maximum Likelihood tree, my Log Likelihood is -24465.21, the three were built using the General Time Reversible model, G+I, gamma 6, NNI, 25 threads, and 500 Boostrap reps.
Can anyone elucidate why this is happening and what I should have in mind when constructing the next three?
Thank you very much
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Keep in mind that for a molecular phylogenetic tree to make sense, homologous nucleotide positions (those that descend from a common ancestor) need to be aligned with each other. While we can't directly "see" homology, the degree of nucleotide similarity is the best guide, and is the tool that alignment programs such as Clustal or Muscle use. If you constructed your tree with no gaps, as you put it, it sounds like you've made no attempt to do this.
You don't describe what locus (or loci) your sequences are from or the length of the sequences. However, I'm guessing these are coronavirus sequences. If a lot of these are SARS-CoV-2, the number of nucleotide differences between correctly aligned sites is still pretty small, so a high-confidence support for most branches simply can't be achieved.
Finally, the cladogram display you're using throws away most of the information from maximum-likelihood tree construction on just how much change has taken place on each branch. A phylogram display would give you that information. I suspect that an aligned set of sequences would show a lot of very short branches, consistent with the things I mention in the previous paragraph.
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We used a single locus analysis (ITS) for the provided set of FASTA sequences. We're hoping you could give us advice or tips to make a cohesive interpretation of the phylogenetic tree given the limited data that we have which are morphological characteristics and genetic sequences only.
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For phylogenetic analysis is better to generate the Bootstrap tree and PP tree. Fasta file can be changed to Nexus or Phylip files for MrBayes and IQTREE (e.g. in Mesquite, PAUP, etc)
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I'm working with sequence data from a set of closely related species and along with other indels and SNPs there are microsatellites regions in the sequences.
I was planning on building a character matrix using complex indel coding, which from my understanding requires the sequences to all share a 5' or 3' end. Where I'm running into trouble is that there is some variation in the repeats as well, with the occasional insertion or deletion giving me trouble aligning (ex. the repeats are mostly AT but there's the occasionally extra A or T).
I can't only rely on the microsatellite data, so is there a way to build a character matrix that differentiates the taxa based on the repeat number and the variations in them (insertions, deletions, and substitutions) rather than just depending on the length?
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Hi,
I am not sure if it fits your goal but you can check Müller 2006
Hope it will help.
Best regards,
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Hi All,
Are you an expertise in getting ancient DNA? Currently I am looking researchers who have expertise in getting DNA from old herbaria collections. Even better if you have it with Ascomycota (Fungi). If so and you like to collaborate with taxonomist to work in projects about systematics, evolution and biogeography, please contact me at lquijull@gmail.com or luis_quijada@fas.harvard.edu and write in the subject of the email "ancient DNA". I am looking for collaboration to learn these technics but also you will be coauthor of the results of this project that start in July.
Best wishes
Luis
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we have extracted DNA from ca. 30-50 years old herbarium basidio samples including some types, though this age is not that “ancient”…
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The new variety is being of natural hybrid origin and it has ornamental values. It has not been described or discovered before as far as I have concerned.
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Hi
after register, published it.
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The website for the web interface for the genealogical sorting index (gsi) is down, and it seems hard to find the r-package as well. Therefore I need an alternative. What do you suggest? I need to test whether morphotypes, as well as ploidy levels are sorted according to the phylogeny, in all may cases they don't seem to be monophyletic, but I see a pattern, but I need to test it it is significant.
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Hi Svante,
I know it's been over a year, but just wanted to let you know that I wrote my own implementation of the GSI on an R package of mine. Check it out here:
You can install it with:
remotes::install_github("santiagosnchez/rBt")
library(rBt)
Then the gsi function would work with something like:
tr = rtree(10)
groups = split(tr$tip.label, factor(rep(c(1,2,3), c(3,3,4))))
tr_gsi = gsi(tr, groups)
tr_gsi
Let me know if you run into trouble.
Santiago
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Hi, I can't find published papers using the make.simmap function in phytools (R) for discreet characters, however it is supposed to implement a similar method to SIMMAP 1.5 and it runs better then the original program. I've had problems imputing a matrix with uncertainties (?) in SIMMAP 1.5, and have to manually edit a huge matrix every time I run the program. Any reason to prefer the original program instead of Revell's function for R? Has anyone tested both with similar results? Thanks a lot.
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Hi,Noemy Seraphim.
Simmap offical website is not available. I can't download Simmap software.Do you have the download link or installation package of it ?
Thanks
Ru.
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How do we select the best outgroup for constructing phylogenetic tree? Suppose if my isolate is gram positive. Can I select the outgroup from gram negative group.
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Can I use a fungus as an outgroup for my Gram positive bacterial phylogenetic tree?
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Sequenced a marine actinobacterium for 16S, assembled and identified in Eztaxon. Obtained 98.58% similarity with Citricoccus yambaruensis. Can it be a new species? Can I go for whole genome sequencing to find out the novelty?
Seeking for valuable comments and directions...
Thanks in Advance.
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what about whole Genom ??
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The question stated above is the title of a book review (see http://www.journals.uchicago.edu/doi/pdfplus/10.1086/694936?utm_content=bufferaebfd&utm_medium=social&utm_source=linkedin.com&utm_campaign=buffer ). I thought it would be interesting to read both opinions about the book reviewed ("The Future of Phylogenetic Systematics: The Legacy of Willi Hennig.") and colleagues' own answers to the questions: "Does the Future of Systematics Really Rest on the Legacy of One Mid-20th-Century German Entomologist?"
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The question posed by David Baum in the title of his book review, "Does the future of systematics really rest on the legacy of one mid-20th-Century German entomologist?" is deliberate distortion of our book's title, :The future of phylogenetic systematics: the legacy of Willi Hennig." The book is comoosed of contributions from a Linnean Society symposium that celebrated Willi Hennig's 100th birthday, and it was the organizers' intent to mark his legacy with a book that both looked back at Hennig's historical impact on phylogenetics, and tried to assess how his contributions are still relevant today. All the plesion discussion above is a distraction that has nothing to do with either our book or with Baum's review.
Does the future of evolutionary biology rely on the contributions of one 19th Century English biologist? Does the future of physics rely on the contributions of a 17th-Century English physicist/astronomer? Probably not. But that does not mean that we do not honor the contributions of Darwin or Newton or deny that subsequent work "rests on their legacies." As Newton himself said, "if I see further, it is because I stand on the shoulders of giants."
The fact that people are still arguing about whether or not classifications ought to be based on monophyletic (in the Hennigian sense) groups is a pretty clear indication that Hennig's ideas remain pertinent in the 21st Century.
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Hello,
I´m including P. orbignyi in a population analysis for conservation genetic study. In GenBank are a few sequences; but, into them, there is not any sequence from Brazil, where was originally described the distribution of this stingray. And it is important in order to used as a start or reference point f genetic analysis. 
Thanks!!
Angelica
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Andrey, thanks so much! I'm using them...
I´m looking for Tocantins sequences where were described the Holotype
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Start Period of rattans evolution in Indian phytogeographical zones?
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A quick look through Saxena and Trivedi's Catalogue of Tertiary spores and pollen from India for Dicolpopollis spp (dispersed pollen of Rattans) reveals many records from the Middle Eocene onward, but virtually no records from the Paleocene or Early Eocene (a couple of records such as 'Dicolpopollis spp, Paleocene-Eocene' for instance need to be checked out for both the actual age of the sediments and the attribution to Calamoidae) .
Rattan pollen first appears in the Maastrictian of the Horn of Africa, and is also present in the Paleocene of Sarawak, so the possibility needs to be raided that Calamoids dispersed into India from Asia following collision, and might therefore be an 'into India' immigrant!!  
The oldest records of Calamoid pollen in India therefore needs to be carefully checked to comfirm or refute the possible Middle Eocene first appearance
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There are many methods used in phylogeny viz. Maximum Likelihood Tree; Neighbor-Joining Tree;   Minimum evolution Tree; UPGMA TREE & Maximum Parsimony Tree.
I have simply two questions
Whats a criteria for new species and how molecular studies will support?
Which will be best method for species relationship or identification of new species/genus?
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Parsimony is outdated. Go for both Maximum Likelihood (ML) and Bayesian analyses.
For ML analysis can use Garli, RaxML or IQTree. For Bayesian try MrBayes or BEAST.
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I need compare a particular protein coding (nucleotide) sequence and amino acid sequence with vertebrates and non-vertebrates and understand the mechanisms of evolution and relatedness using phylogenetic analysis. I'm confused between distance methods, parsimony, maximum likelihood, and neighbor joining methods for correct analysis. Also how to interpret the phylogenies and construct trees for the nucleotide and amino acid sequences. Kindly suggest me on the problem and right computational tools for the analysis.
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Hi Puneeth
How are you doing?
There are many tools available online for multiple sequence alignment and phylogenetic tree construction.  Selection of different methods depends on your objective.
Have a look at this site. http://molbiol-tools.ca/Phylogeny.htm
If you need any clarification call me.
regards
Jayaram C
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My lab mates and I unable to conduct an SH test in RAxML on CIPRES. We have used a .phy file for our input, deselected "Configure Bootstrapping," supplied our best tree in a .tre file from our previous run using the same .phy file under "Simple Parameters', selected "Compute a log likelihood test," supplied our "Bootstrap_Result" file. Did we miss a step/is there a better way to do this?
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I think the SH test in RAxML need two trees, and I'm not sure if it can compare a best tree with the bootstrap trees in this way. In the command line would be something like this  raxmlHPC.exe -­f h -­t ref -­z trees - ­s alg ­-m GTRGAMMA ­-n TEST. As it not estimate the trees again (just optimizes the lk for the trees) is a fast analysis to run even on a laptop (if your alignment is not enormous)
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I'm a bit suspicious to that tree, to me it looks odd to have A0 being separated from Aalba with such a relatively long branch and still not have Aalba monophyletic. What methods is the tree estimated with and is it correctly rooted? I would guess you may get a different result if you reestimated the phylogeny with a different method and if needed additional outgroups. But as already said Aalba is paraphyletic and A0 is monophyletic in your tree
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The aims are to know relationships among individuals in one species and to classify into two groups: good and bad individual which will be used to increase a population and to control it.
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If you look for overall correlation between morphological and genetic data for the same sample set, you shold perform Mantel test. All you need are the distances (or similarities) between the accesions. I would suggest R package ade4 to do this.
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Hi
I want to reconstruct the phylogenetic trees of plants and insects.
What genes do you suggest when reconstructing the plants(Moraceae) phylogenetic tree? I have used the ITS, G3pdh, GBSSI, ncpGS and ETS, but there are some problem when sequencing. Is there are something wrong with my gene?
As for the insects (Hymenoptera), I want to use the mitochondrial cytochrome c Oxidase subunit, and what gene & primers do you suggest?
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The choice of gene depends on many factors. I work on plant phylogenetics specifically Solanaceaea, Malvaceae and Convolvulaceae. I have tried rbcL, matK, ITS, and some intergenic spacer and all worked well in term of sequencing. The resolution power of a marker accounts for what relationship we want to infer. 
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Morphological characters recorded include colony type, slerite form and size, colour.
Which software do you recommend?
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MrBayes can use morphological data.
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I have a maximum likelihood tree (18S and COI) for a nematode family which contains 4 different genera. The bootstrap values were very low and all the 4 genera are intermingled in both trees with no separation per region or genus. Does this mean that the genera separation is not supported?
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Hey Lidia! Low bootstrap values indicate that there is conflicting signal or little signal in the data set. This may be a problem in the alignment, as Chris suggested. In this case it could be due to an erroneous alignment, which often occurs when the sequences aligned are ambiguous or too diverse. Sometimes, different clades had different rates of evolution (more or less mutation when compared to each other). Also, the absence of intermediate taxa could be a problem. Alternatively, information may be simply absent or too low in your alignment. That is the case when a very conserved DNA fragment has been used and sequences are too similar to each other. Normally you cannot conclude much else from low bootstrap values.
Normally, if a node in the dendrogram is not supported (usually bootstrap below 50) you cannot trust the bifurcations and that is why usually these nodes are collapsed in a tree graph to form a polytomy. If a node is poorly supported (50 to anything around 85 - a bit a case of personal interpretation, I think) it is to be treated with care but there is some support at least. Anything above that value can be interpreted with confidence.
I guess that your COI tree will have problems predominantly. Here, due to the protein-coding nature of this gene, the alignment should not be a problem. However, the third codon position may lead to "background noise" in your data because of the saturated code and silent mutations. A way to improve your results may be to infer relationships again with the third codon positions excluded.
As for the robustness of the concepts of the genera you study: you may doubt it is, as you wrote, they rely on poor descriptions. Think about the apomorphic morphological characters: are they complex characters, or is there evidence that they may have evolved multiple times independently? Usually, a taxon defined by more and more complex characters is more robust. I would not accept my molecular results blindly, but investigate, if they are plausible given alternative data (morphology). If so, robustly supported clades in your dendrogram that show polyphyletic or paraphyletic genera disconfirm the generic concepts and you can with confidence hypothesize that the genera should be systematically revised.
Hope that helps! Cheerio!
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More specifically, the details and reasons for its numerous synonyms.
Sources are welcome.
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The main revisionary study that treated the synonymy of C. niger was Haedrich 1967:
Haedrich, R. L. 1967. The stromateoid fishes: systematics and a classification. Bulletin of the Museum of Comparative Zoology v. 135 (no. 2): 31-139.
You will find all the details about Centrolophus niger (Gmelin 1789) and its junior synonyms in the Catalog of Fishes online,
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Which mouse and which rat? The terms "mouse" and "rat" are polyphyletic and do not correspond to phylogenetically informative groupings. There are multiple families which contain taxa called mice and rats- New World mice and rats, Old Worls mice and rats, Neotropical mice and rats, etc. Here is the current topology from the Tree of Life project: http://www.tolweb.org/Muroidea/16461
With that being said, I am going to assume you are talking about Mus and Rattus... Here is a recent paper on adding additional evidence to amend the previously held 12 my split:
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Basically, there are three modern schools of taxonomy: cladism, evolutionism and pheneticism. While the debate continues between the first two schools, did the third one completely faded out? If so, what was the last paper or the last book published advocating this classification scheme? If not, who does still advocate it?
EDIT: My question has been misunderstood by some. I am asking if you know someone or some modern papers promoting polyphyletic taxa in classification (= pheneticism) like Sneath and Sokal.
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I respectfully submit that Frank has missed the point of the original question. Phenetics was a methodology, not a description of characters. It was the grouping and classification of organisms based on overall similarity, as opposed to Hennig's phylogenetic systematics (which became known as cladistics) which used special similarity (synapomorphy) to group and classify organisms. Those were the competing paradigms and while Hennig's basic ideas certainly won out over phenetics (see D. Hull's great book Science as a Process), phenetics is back on the rise. With the accumulation of massive genomic data sets, some folks are turning to phenetics as a way to analyze these data sets. 
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Hi everyone,
Recently,I read many papers about the selection pressure.In some papers,the author use the Codeml soft to detect the selection pressure of the internal and external in phylogenetic tree .I don't know the meaning of "internal"and "external",what's more,how do we set up the two in our phylogenetic tree and use the Codeml to detect them?
Thank you very much for your all answer!
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Hi Mark,
    Thank you for your advice but I need know the mean of internal or external  select pressure because I also need to use it in my paper analysis.
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What are the most state-of-the-art methods to build a phylogeny with missing data? I have a 12 genes and 50 species, but some genes are missing for some taxa. There are genes were have only little coverage. Supertree? Supermatrix?
In some cases I have more than one allele for a given gene. Can I somehow incorporate this to the final tree? e.g. LFY Allele A and Allele B for Species A, GBSSI Allele A and B for Species B, while other species have only 'Allele A' only...
In some cases I have duplicate sequences from different individuals of the same species. e.g. 3 ITS for species A, 5 GBSSI for Species B, 1 trnL for Species C etc. Is there a way to combine them together in one analysis?
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Different genes evolve at different rates.  It is possible to build trees from a mix of data such as you are describing, but the results need to be understood in the context of the data used.  With the explosion of data available in databases today, it is quite common to see researchers gathering large but sparsely populated data matrices from which to build phylogenies.    The resulting trees quite often have some species on long branches because only rapidly evolving genes (mitochondrial genes for example) were available from those species while other species are on short branches because only more conserved genes were available, and I have seen authors claim that this indicates different rates of evolution of the species as a whole when in fact it does not.
Most phylogenetic methods require that there be at least some overlap of comparable sites across all species in the set.  And it may be more instructive to build a tree from each gene and then compare the trees, than to attempt to build one supertree when the  larger set is a sparsely populated matrix.
It is a little difficult to give advice in general about such things, because not all types of organisms have similar evolution.  For example some species have more geographical or other barriers preventing gene flow between populations as they evolve.  Are you dealing with viruses, plants, fungi, bacteria, vertebrates, insects?
One example I am familiar with, which has their complete data matrix available in TreeBase so you can explore it, is a study of avian evolution by Hackett et al 2008:  http://www.sciencemag.org/content/320/5884/1763    http://treebase.org/treebase-web/search/study/summary.html?id=11811
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This work really reflects a consensus of the work done on this issue?It has any connection with the theory of endosymbiosis? There is a phylogenetic relationship from its origin? Be right handle the classification by or Supergroups Kingdoms?They correlate with studies of genomes of viruses? From that point of view the classification should be done ?.
In the images that I uploaded is a summary before 2015 classification of eukaryotes.
Let's discuss this important topic, thanks for your contribution.
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I strongly disagree with their convention to list all taxa alphabetically. In almost every case there is a wealth of phylogenetic data showing that the taxa listed in adjacent positions in their linear classification are actually not closely related.
An example from birds: Psittaciformes (parrots and allies) is now known to be the sister taxon of Passeriformes (the songbirds), but these are not listed next to each other in this classification. Any classification that does not reflect such knowledge, is not going to be taken seriously by specialists and is doing a disservice to its (non-specialist) end-users.
And even if taxa are correctly placed next to each other in a list of multiple taxa, they could not be placed in a separate taxon because the relevant rank was not used by the authors. For instance, Archosauria (the clade containing crocodiles and birds) could not be recognized. Thus, the new classification disregards a huge body of knowledge because the authors limited their endeavor to a small number of ranks.
This is a classification of living organisms but it is unlear how extinct clades can be accomodated in this system. This is not a trivial issue given that >95% of taxa are extinct. For instance, Aves (birds) is listed as a subclass of Reptilia, but there is no indication how the large number of splits in the phylogeny between the origin of Reptilia and the origin of Aves are going to be ranked.
Another problem is how sister taxa are listed. If two taxa are sisters, current practice (albeit mostly implicit) is to list the smallest clade before the largest. In ornithology, ALL modern authors place Palaeognathae (ostriches, kiwis, etc) before Neognathae ('modern' birds) because the former is the smaller clade. In the classification by Ruggiero et al. (2015), the order is reversed because N comes before P in the alphabet. I doubt that anyone in ornithology is going to use this.
This could have been avoided (i) if the ambitions of the authors were a bit higher, (ii) if the level of detail (structure) of the classification was based on actual phylogenetic knowledge, rather than a small set of ranks, (iii) and if the authors had sought the help from specialists.
A rankless system (i) would have given the authors the freedom to recognize additional clades and resulted in a much better reflection of current phylogenetic knowledge, and (ii) avoided pointless 'debate' about the 'appropriate' rank of any given taxon.
However, even with a ranked system much more could have been done with all the phylogenetic knowledge that is already available.
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I want use outgroup for these bacteria.  and  I don't know is this possible that I use all of them in one tree?
Pseudomonas chlororaphis
Pseudomonas putida
Pantoea agglomerans
Stenotrophomonas maltophilia
Chryseobacterium elymi
Rhodobacter ovatus
Rhizobium sp.
Bacillus infantis
Bacillus cereus
Microbacterium oleivorans
Guide me please...
Regards
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It is possible to construct a phylogenetic tree across even greater diversity than the eubacterial species you are describing here.  For example, it is possible to make a tree including eubacteria, archaebacteria, and eukaryotes.  Using ribosomal RNA sequences (or the genes endocing them) plus genes for DNA polymerase and other highly conserved genes that are very often sequenced from many different species, and which tend not to be horizontally transferred between diverse groups, is important.  With a diverse group of species such as those on your list, the choice of an outgroup depends on why you want to use an outgroup.  A good alternative is to use midpoint rooting for your tree.  No matter what bacteria you choose for an outgroup, you are likely to create a "long branches attract" problem where the outgroup will join this group on the longest branch within this group (the ingroup).  This will tend to bias your view of the evolution of this ingroup if you do not understand the long branches attract problem.
Another potential issue to deal with is to make sure that genome composition bias (A+T rich organisms, compared to G+C rich for example) does not bias the results.  Bacteria can have very large differences in DNA base composition which can tend to make the AT-rich organisms group together away from the GC-rich ones, or at least bias the results if there are both types of genomes in your data set.  The DAMBE phylogenetic analysis package has some good tools for exploring other aspects of the data, in addition to providing phylogenetic analyses.
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How can I use the RAST annotated microbial genome data to study phylogenetic relationship of a particular gene with other closely related organism?
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I am not entirely sure what data you have and what you are looking for. I infer that you have a genome annotated through RAST and want to compare a particular ORF/gene with other taxa for which you do not presently have genomes/the gene of interest. If this is the case, I would extract your gene from RAST and BLAST it against the non-redundant database on NCBI. You can then align and infer phylogenetic reconstructions from this data or any number of other analyses.
If you have other annotated genomes you particularly wish to compare (and especially if there is other genomic analyses you will wish to perform) clustering the genes into homologous groups is an excellent first step. For this I 2nd Danielle Cloutier and recommend GET_HOMOLOGUES as an excellent and user-friendly program. You can then extract the HG(s) containing the gene(s) of interest and proceed with those sets.
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While analysing dataset on MrBayes for phylogenetic analysis, how one can determine the length of the burnin period?
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I would suggest to check your run files either MrBayes or Beast by importing into Tracer where you can actually figure out to set up burn-in.
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I'd like to amplify Archaeal 16S in order to do phylogenetic analysis. I know that for bacteria the standard primers are 27F and 1492R, but I would like to know which ones are used for Archaea. 
Thanks, 
Mario
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Please refer our paper "Haladaptatus pallidirubidus sp. nov., a halophilic archaeon
isolated from saline soil samples in Yunnan and Xinjiang, China
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I mean can molecular data tell the authenticity of subspecies in a taxon ? Like it is a convention that difference of 2% genome leads to distinction of two populations as a separate species. Can it be inferred that between 1.5-2% difference in genome leads to conclusion of sub species ?
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Hello Harsimran,
I understand what you are asking and why, but I think it is perhaps worth while going back to the pre-molecular era and considering what subspecies were designed for - I say "designed for" because they are of course a taxonomists' concept, not a biological one.  Classically, subspecies are geographical races of a widely distributed species which are reliably distinguishable on some morphological character or character set. I suppose you could translate this into molecular terms by saying that a subsp. is a geographical race  of a species with a distinctive sequence.  However, the two critical components are a) the geographically limited distribution and b) the distinguishability. In my own work (on grasshoppers) I was able to show that previously described subspecies  were all  significantly different from each other in some morphological parameter. However, the differences were not enough to RELIABLY assign any individual specimen, as  the variance within the individual subspp. meant that there was always overlap. Only one population was so different from the nominate race that all its members could be reliably assigned to its (geographical) source, and that was the only one that I recognised as a subs. in my revision. If you would like a copy of that paper, let me know.   Hugh Rowell.. 
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I would like to find taxonomic solution for the insects ie. aquatic bugs (Naucoridae) I am working with.  I have already decided that I am going to approach with the genes of 16S rRNA and 28S rRNA for the aforesaid after went through the previous attempts of works related to this. Eventhough, I am looking for the valuable suggestions from the scientific communities those who are dealing with the related issues.
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The choice for genes should be based on the taxonomic range you are interested on, for instance 16S can be considered to investigate deeper nodes, e.g. between tribes or subfamilies, whereas 28S for intermediary nodes, e.g. between genera within a tribe or subfamily. If you want to investigate the relationships within a genus you should think about using COI, COII and Cyt b for better ingroup resolution, in combination with 18S and 28S for outgroup resolution.
You can find interesting results about these topics here:
I also agree with Eduardo that using an integrated approach will give you more informative results.
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Hi everyone,
I am trying to build a phylogenetic tree with a few hundred 16S sequences of different sizes. About half my dataset is around 700 bp, the rest is complete sequences (around 1500 bp).
Obviously, when I align these sequences, a lot of positions are going to consist in gaps for half of my sequences.
I don't know what is going to hurt the quality of the final tree more : leaving these gaps, which don't really provide information and can lead to "wrong" clusters, or removing these positions, which comes down to removing information for the sequences that did have a base.
I guess another way to ask this question is to ask : is it a bad idea to try and make a tree with sequences of different lengths? Is there a way around these technical issues?
Thanks a lot for your help,
Marine
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Hello Marine,
There have been several great post so far for this question and you are probably bombarded with information right now. There are also plenty of examples out there in the literature where missing data did and did not affect the final typology. For me sometimes it helps to carry out an experiment on my data to truly understand how missing data will affect a tree. For example you can make a phylogeny with the follow three data sets and compare the results.
1) Only samples with complete sequence.
2) All samples cut down to 700bps.
3) All samples with missing data.
If all the topologies are the same then missing data may not be a big deal. If the topologies are different then you get a better understanding of how missing data affects your results and can make a better discussion on what to do next.   
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I retrieved 1500 sequences (from NCBI) of 6 different protein isoforms belonging to metazoans. Now, the issue is if it is possible to deal with such a large number of sequences in order to reconstruct the phylogenetic tree. What could be a clever strategy? Does this number pose challenge for dedicated software like PhyML, MEGA or MrBayes? What kind of these software should I use?
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Certainly lot of software will handle 1500 sequences. The question is whether the results will be interpretable or reliable. I would think that across such a large group, that the evolutionary processes will not be similar. In other words finding a model of sequence evolution that fits such a large variety of taxa could be difficult. And yet if the proteins are reasonably conserved it may work. I would start out with a neighbor joining tree to see if the relationships make any sense and to check that the alignment for so many taxa is optimal. Then, for the search, use maximum likelihood methods in Phyml, which is fast and reliable. The implementation in Seaview is handy since you can align and optimize in the same program.
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I want to perform phylogenetic analysis for a large number of protein sequences from banana. I have tried using few softwares but not able to get any reproductive data. Can anyone suggest me the apt. software to be used ? Thanks.
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Try our MetaPIGA software: http://www.metapiga.org.
Best, M.
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Moniliformis moniliformis might be the most likely species. The hooks in the proboscis is important in some literature, but it is difficult to distinguish since they do not seem to form lines.. 
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I suggest you to write Dr. Omar Amin. He es an authority in this gropu of species
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Looking for something similar to the Phylogenetic tree, but for technology. For reference: 
  1. http://en.wikipedia.org/wiki/Timeline_of_historic_inventions
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A "tree" structure makes a lot of sense for most carbon-based life forms because we all come from parents.  There is some horizontal gene transfer but the core of most genomes evolved from ancestors in a tree-like manner.   Technology and human social evolution is far more network-like.  Automobiles today are not just descendants of the Ford Model A, they use plastics and other materials from the materials sciences, computers to control the engine from the computer sciences, aerodynamic design from aerospace research and so on.  Thinking in terms of "tree" structures may impose limits on your ideas that a network design would not.   See for example: https://johncarlosbaez.wordpress.com/2015/04/04/categorical-foundations-of-network-theory/
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from Pakistani waters
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Rhopilema hispidum
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In Genious I am getting the message "PAUP* block is illegal for the following reason: If you are doing bootstrapping, you must specify the file to save the boostrap consensus to."
I don't know if my block have errors:
SET AUTOCLOSE=YES;
SET CRITERION=PARSIMONY;
SET ROOT=OUTGROUP;
SET WARNTSAVE=NO;
SET INCREASE=AUTO;
OUTGROUP taxon1;
LOG STAR FILE=ITS_parc.out;
[consenso 1_1]
HSEARCH START=STEPWISE ADDSEQ=RANDOM NREPS=2000 SWAP=TBR;
DESCRIBETREES 1/PLOT=PHYLOGRAM BRLENS=YES ROOTMETHOD=OUTGROUP OUTROOT=MONOPHYL;
SAVETREES FILE=ITS_parc_1_1.tre BRLENS=YES FROM=1 TO=1 ROOT=YES;
SAVEBOOTP=NODELABELS MAXDECIMALS=0;
CONTREE ALL/ MAJRULE=YES PERCENT=85 TREEFILE=majrule.tre;
SAVETREES FILE=ITS_parc_1_1_contree.tre FROM=1 TO=1 ROOT=YES SAVEBOOTP=NODELABELS MAXDECIMALS=0;
[bootstrap 1_1]
HSEARCH ADDSEQ=RANDOM NREPS=2000 SWAP=TBR;
DESCRIBETREES 1/PLOT=PHYLOGRAM BRLENS=YES ROOTMETHOD=OUTGROUP OUTROOT=MONOPHYL;
SAVETREES FILE=ITS_parc_1_1.tre BRLENS=YES FROM=1 TO=1 ROOT=YES;
SAVEBOOT=NODELABELS MAXDECIMALS=0;
BOOTSTRAP NREPS=2000 SEARCH=HEURISTIC;
SAVETREES FILE=ITS_parc_1_1_cboot.tre BRLENS=YES FROM=1 TO=1 ROOT=YES;
SAVEBOOTP=NODELABELS MAXDECIMALS=0;
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Why don't you try PAUP 4.0 directly. An HSearch will give you your answers. You can also do your bootstraps, it's easier. You just have to convert your file as Nexus, or if its already in Nexus format, that's fine. I think PAUP is itself a very robust program
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I have a plan to conduct a study about the different cultivar of cassava found in Romblon. And, to determine the phylogenetic tree of cultivar, what kind of morphometric analysis should I use?
Thank you.  :)
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I am planning to use a Traditional Morphometric Analysis to determine the quantitative measurement of morphological parts. If I already get a morphometric data, is it applicable to undergo a phylogenetic analysis to determine the evolutionary relationship of a different cultivars of Cassava?
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Is is legitimate to use geographic occurrence, specifically altitudinal/bathymetric range of species, as character states to use in an ancestral-states reconstruction? Can origins be inferred this way? Are there examples in the literature?
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I think very interesting placement of Crother. However, I worry how this is being done today. I think that current approaches are too simplistic. Do not take into account a number of empirical knowledge that we have about the distribution of species. Thus, what I mean is: It may even be possible to estimate an ancestral area, but it is not a simple task as rebuilding an ancestral state of a character in a phylogeny (at least in the most cases).
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Phylogeny indicates a deep node between clade for Sturnidae and basal Rhabdornis clade in Zuccon, Dario; Cibois, Alice; Pasquet, Eric & Ericson, Per G.P. (2006): Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa. Molecular Phylogenetics and Evolution 41(2): 333–344. Still, the placement of Rhabdornis within Sturnidae requires confirmation.
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In Vol. 2 of the Howard & Moore Checklist (ed. 4) published in October we accepted one family fo starlings and treated Phabdornithinae, Mainatinae and Sturninae as the other subfamilies. See Jeol Cracraft's chapter and the tree on p. xlv.
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What is a factor one should improve to increase a efficiency, robustness and sensitivity of a phylogenetics pipeline with an algorithm?
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Hi,
It is well known (I believe) that bayesian algorithmes is much better but also much more computational  expensive. The model should be validate by a cross-validation. For the overall robustness it is important to produce a bootstrap analyse. You may take a look at Phylobayes http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm.
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Can I Use the EzBiocloud assemble service to merge F and R sequence? I heard that this will remove the bad sector sequences by automatic trimming and mergin them together. My question is: Can I use the assemble service to merge my sequences (Good quality sequence) when looking for new genuses? Kindly any one help me to fix this. This is very much important for my research. I hope some experts will give me a lead.
Thanks in advance
Regards
Siva
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In the past I did this manually by aligning the forward and reverse sequences and complementing one sequence with data from the other. In the meantime I am using BioPerl to create consensus and IUPAC consensus sequences to check for discrepancies or polymorphisms. I never used the service you mention. If you want to make sure that the service delivers reliable results, just compare the result with the raw data.
Cheers
Thomas
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This is the phylogenetic tree constructed by a company using MEGAN 4.70.4, but I am not sure how to interpret the value. Can anyone explain to me?
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A phylogenetic tree is composed of branches (edges) and nodes. Branches connect nodes; a node is the point at which two (or more) branches diverge. Branches and nodes can be internal or external (terminal). An internal node corresponds to the hypothetical last common ancestor (LCA) of everything arising from it. Terminal nodes
correspond to the sequences from which the tree was derived (also referred to as operational taxonomic units or ‘OTUs’).
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Can anyone interpret the phylogenetic relationships for species J and species K (labelled as J1-J3 and K1-K3)? Both species are morphologically identified as distinct species. Gene A cannot differentiate both species, but Gene B SEEMS to differentiate slightly? Can anyone lend me your expertise? Thanks.
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Stanley: you should use other types of phylogenetic analyses, as Maximum Likelihood or Bayesian Inference. In my opinion, NJ is good for a first approximation to the sequences, but not for constructying strong phylogenies. In any case, surely you would get lower bootstrap and bayesian posterior probabilities.
And no: you cannot say that with gene A K is paraphyletic: is polyphyletic (diphyletic, in that case). 
Hope this helps.
Arthur: with the information Stanley provided (we don´t know the gene, we don´t know the taxa, more information about the divergence between the sequences is lacking...), it is impossible for me ascertaining if these two species are a single species or syster species. The cladograms don´t show monophylethic syster clades and enough support for the clades is missing. Can you provide any further information about how you reached your opinion? Thank you.
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I'm using the "traditional search" on the TNT. Even after do optmization of characters, the found trees have bad parameters, for instance: Length = 79 ; CI = 0.4 ; RI = 0.7. Perhaps using another algorithm, these parameters change.
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If the matrix (specifically number of taxa) is small enough, you could try implicit enumeration, the equivalent of branch and bound in PAUP*. Unlike traditional search, it will always find all shortest trees, guaranteed. The main problem is that it takes longer than the other types of parsimony searches, so it is only reasonable for small numbers of taxa.
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I am working on success rate of DNA barcoding in identification of species using distance and tree based methods.
Regarding distance based method, I have used Adhoc and species identifier and confirmed species identification using best closest match criteria (BCM).
Please suggest program/software/method for tree based identification (using NJ, parsimony, bayes), exhibiting clustering (number of clusters formed for particular species) that will suggest singleton (=Ambigious) species. (Pls see the attachment)
(Please Note: It is not possible to do it manually as iam having >4000 specimens)
Answers detailing methods or softwares is appereciated! Thank you!
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I believe the only accurate method would be alignment-based phylogenetic analysis based on likelihood (e.g. RAxML on a public server such as CIPRES for such a large dataset), combined with a GMYC approach. Anything else, including and particular clustering and NJ methods, have been shown to be inaccurate, sometimes substantially so. Also, if you actually want to TEST barcoding accuracy, you need a testable expectation. For example, you have a set of barcoding sequences for KNOWN species (or at least species-level clades), based on a reconstructed phylogeny. Then you randomly select a sequence and blast it against the entire dataset and see how often the correct species is blasted. That is kind of trivial but that would be the only way of testing. If you have a set of unidentified barcoding sequences and just want to see how many distinct species you have in there, that would not be a barcoding test but an assessment of species delimitation. A very quick approach to sorting out species would also be using MAFFT with the sorting option, which will align the sequences and also sort them based on similarity. It is not 100% accurate but usually, especially if all sequences are complete, does a great job in outlining possible species-level clades even before running a tree. And 4000 sequences can be easily done in MAFFT.
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I have been interested on the theoretical foundations of the Systematics, especially when this area meets molecular biology and started to ignore other information sources as chromosomes or morphological traits.
This union was very strong and congruent with the neo darwinian definition of evolution as a process of change in the frequencies of alleles. But in my opinion the causal pluralism that defend the Developmental systems theory in the relation Genotype-Phenotype (and additional critics and proposal as Extended Inheritance) demand a new definition of evolution and by consequence a new systematics framework, that could make clear how build the history of the living things.
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Molecular data is not better than morphology and morphology is no better than molecules.
Despite what Robert said, there is no guarantee that a molecular tree is closer to a "true tree". Also, different fragments may also disagree between each other. Should one discard one dataset? On what basis? There is no such a thing.
Robert, I am sorry, but I don't think your examples are really good. Morphology works really well in deeper levels of the hierarchy, although molecules may be more useful for the shallowest ones. Sharks and dolphins would never come out together in a properly done cladistic morphological analysis. One done with robust primary hypothesis of homology.
Remember that we found out that reptiles, dicotyledons, ferns and other groups are not monophyletic way back when nobody was using molecules.
One thing that tells us that this is just molecular convergence is morphology. Bats and dolphins clearly do not form a monophyletic group.
Besides, you can have an alignment with more than 3000 bases without variation and that is, consequently, uninformative. Some colleagues are about to publish a paper showing that the whole chloroplast genome of Asteraceae has a very low level of variation and how the effort in sequencing is useless to build phylogenies for anything lower than tribes (and tribes in Asteraceae are kind of big). On the other hand, 30 or so morphological characters can have a lot of information.
I do think its is more than time for us to stop arguing what kind of data source is better and to join efforts to use all the good information we can get our hands on in total evidence analysis.
Of course "good" may mean different things for different people, but check that:
Cheers, you all,
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The RelTime algorithm of Tamura et al. (2012 PNAS 109:19333-8), has been available for some time in MEGA6 but I see few people using it. Why is that? What concerns do people have with this method versus BEAST / R8s / PAML?
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I think this is just a question of response delay. The article was published late in 2012, so for anyone using the method and publishing an article by itself, you would have to expect at least 12 months, more likely 18-24, for such a new method to "take off". The method itself is solid and has been tested with simulations and in my view is as good or bad as any sophisticated molecular clock approach, since all these approaches work with assumptions that might not necessarily be close to reality. Any such method has to be used with caution, but on the other hand, in the absence of a complete fossil record for a group of interest, this is as good as it gets. The big advantage of this new method is that it works with much larger datasets, which might also explain why only few papers using this method have been published so far.
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If I have two species belonging to the same genera, let say species A and species B, if species A has 3 specimens and species B has 4 specimens when calculating the genetic distances within the species there will be a total of 9 comparisons. That is 3 comparisons for species A (A1xA2, A1X A3, A2XA3) and 6 comparisons for species B (B1xB2, B1xB3, B1XB4, B2XB3, B2xB4, B3xB4).
Does anyone know if there is software which can calculate the total combinations?
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I have seen that in some publications, they give this info when they do plot for % frequency against % genetic distance for comparison between intraspecific (conspecific) , interspecific (congeneric) and confamiliar variation among the sequences.
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Some bacteria have very high species diversification with various phenotypes and genotypes. For example, Bacillus subtilis have a lot of subspecies and strains carrying different properties such as enzyme production. Strepmyces is another example with lots of species and subspecies. What are the reasons? Does it mean that those bacteria are more active in gene exchange? Does it mean they are evolutionary more dynamic than other bacteria?
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This is a difficult question. We tend to ascribe variability within a given taxon to differing mutation rates between taxa and also to different selective environments, a given organism may live in.
All this may be true of course.
However, one of the major reasons for differences in variability is the species definition itself. Most of them, especially in the bacterial (and fungal) world are very broad, including many different genotypes and also different phenotypes. Other species have comparably narrower borders, and, consequently show lower variability.
Without knowing really a lot about the taxa to be comapred, reasonable opinions on variability are hard to establish. I recommend to be very cautious in this respect.
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I found in MEGA5, after bootstrap test, there was no scale bar in my bootstrap consensus tree. While in the original tree, there was a scale bar. Does anyone know why this happens in MEGA5?
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With RaXML, you can search for the best ML tree and bootstrap on the same run, and it will give you a file with the best tree (with scale bar) and the bootstrap values as branch labels.
For the rest, I agree with Brian.