Exchange knowledge in the field of molecular systematics, phylogenetic reconstruction and their application to systematics, biogeography and evolutionary studies

• James Mcinerney

  EMBO have provided some support for a course on "Postgenomic Phylogenetics" in 2013 in Erice in Italy. I will post more information on here as it becomes available. Right now, we only know theEMBO have provided some support for a course on "Postgenomic Phylogenetics" in 2013 in Erice in Italy. I will post more information on here as it becomes available. Right now, we only know the location and that EMBO will provide some funding to reduce the registration cost. http://www.embo.org/myPhpFiles/calendar_ohnewas.php
• Niaz Ali

  Are phylogenetic trees constructed with Maximum Likelihood (ML) algorithms preferred over the neighbouring-joining (NJ) or UPGMA methods?

  I have come come across few statements in articles that suggest ML is preferred other methods of phylogenetic reconstruction, but to be honest I did not see any reason why. I wonder if someone hasI have come come across few statements in articles that suggest ML is preferred other methods of phylogenetic reconstruction, but to be honest I did not see any reason why. I wonder if someone has any suggestions/comments please. Almost 90% of the trees (from 2000-2010) that I come across with have used methods other than ML.

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  • 
    Nauf Alsayaid replied

    @ Nazir Ganai very kind of you...........

    2 hours ago
• Hari Krishna

  Is it possible to speedup the phylogenetic trees construction using MrBayes 3.2.1

  I am trying to construct phylogenetic trees using MrBayes 3.2.1 with highly diverged set of 148 sequences with alignment length of 300 with default options and mixed model. The tree is not convergingI am trying to construct phylogenetic trees using MrBayes 3.2.1 with highly diverged set of 148 sequences with alignment length of 300 with default options and mixed model. The tree is not converging even at 20 million runs and is taking long time. Are there any options to speed up my tree construction?

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    Markus Sallman Almen replied

    I agree that 20 million generations in general should be enough so you probably need to adjust parameters or return to the alignment, which in my experience usually is needed is these cases. Just aI agree that 20 million generations in general should be enough so you probably need to adjust parameters or return to the alignment, which in my experience usually is needed is these cases. Just a few sequences of bad quality can really mess up your run so if possible you should remove these. You can also try to divide it into subproblems according to known subfamilies, species combination etc. If you have multiple cores, CPUs or a cluster you should also compile the MPI version if you haven't already done so to speed it up. I also recommend you to combine MrBayes with a bootstrapped ML analysis and see if you get the same tree. Good luck!

    2 hours ago
• Paula Menna Barreto Dias

  Does anyone know if I can calculate pairwise divergence, number of substitutions and number of indels using PHYLIP?

  my data is DNA sequence (nucleotide) Thanks!

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    Brian Foley replied

    DAMBE is also free, and does many nice analyses. Joe Felsensein keeps his site pretty well updated to list all the packages available for phylogeneticDAMBE is also free, and does many nice analyses. Joe Felsensein keeps his site pretty well updated to list all the packages available for phylogenetic analyses: http://evolution.genetics.washington.edu/phylip/software.html

    2 days ago
• Manan Desai

  Is it possible to generate a maximum likelihood tree using only the active site sequence of the protein and not the entire sequence?

  I am trying to study evolutionary divergence among tubulin family members

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    Manan Desai replied

    @ Douglas, i wish to compare FtsZ (prokaryotic tubulin homologs) with tubulins and compare and see divergence (if any) in the active (nucelotide binidng site) across species

    3 days ago
• Frank Bengelsdorf

  MrBayes3.2.1

  Hello, I am Frank, is anyone using MrBayes3.2.1 around here?

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    James Mcinerney replied

    I must say that I have to disagree with Ijad - UPGMA is an unrealistically simplistic approach and is unlikely to make it past peer-review in any respectable journal, these days. The problem is thatI must say that I have to disagree with Ijad - UPGMA is an unrealistically simplistic approach and is unlikely to make it past peer-review in any respectable journal, these days. The problem is that if there is variation in evolutionary rate among different lineages, then UPGMA is known to be problematic - pushing rapidly-evolving sequences towards the root. I'm also not a fan of NJ, because it doesn't explore treespace, doesn't permit the substitution model to change during the analysis and is not built on the robust foundations of maximum likelihood and bayesian inference, so testing alternative topologies or models is not possible. Model selection is possible using MrBayes and I suggest reading the paper by Ronquist in Systematic Biology in February for some more info.

    4 days ago
• Elson Felipe Rossetto

  Will phylogenomics dominate the systematics research in the next years?

  I saw a paper about relationships in seed plants using phylogenomics methodology. Then, a doubt arose, is phylogenomic methodology more definitive than current molecular phylogenetic methodology?

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  • 
    Ning Zhang replied

    I don't think so. Phylogenomics requires huge data and provides challenge for computing. Phylogenomics sometimes is helpful for deep relationships, however, for most cases, I think several genes areI don't think so. Phylogenomics requires huge data and provides challenge for computing. Phylogenomics sometimes is helpful for deep relationships, however, for most cases, I think several genes are enough.

    4 days ago
• Priyanka Patel

  Phylogeny

  Finding a phylogentic relationship and doing conserved sequence analysis - what else can be done if i have Msa of nucleotide sequences belonging to different species of same phylum?

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    Priyanka Patel replied

    @Ajay sir : Could you plz provide me link for this E-book , Freely Avaliable "Phylogenetic Trees Made Easy : Barry G. Hall"

    Mar 3, 2012
• Arif Tanmoy

  Explanation for Phylogenetic tree

  I am working on some sequences from five different region ITS, IGS, MatK and XTH of two plant genera I have built phylogenetic trees using Maximum parsimony and Maximum Likelihood method by MEGAI am working on some sequences from five different region ITS, IGS, MatK and XTH of two plant genera I have built phylogenetic trees using Maximum parsimony and Maximum Likelihood method by MEGA 5.0. I have already done statistical analysis:mostly Friedman Test by SPSS to compare those trees result came as expected. Now I like to have an explanation about their evolutionary origin and relationship and that's where I am kind of stuck. I just can't realize how to do that. Can anyone here help about that?

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    Fabio Andrade Machado replied

    That's pretty vage, but if you would like to test some hypotheses or origin or adaptation, you should use independent variables (phenotypic, anatomical, physiological, ecological, etc) to do it. IfThat's pretty vage, but if you would like to test some hypotheses or origin or adaptation, you should use independent variables (phenotypic, anatomical, physiological, ecological, etc) to do it. If there is any clear-cut transition of habitats between clades, you could infer that some major change happened there, but that is not accurately testing anything. If you want to talk about evolutionary origin, you should go back to the biology of the groups. There is no magic-pill.

    Feb 6, 2012
• Asha Wadhwa

  Does sequence length change the phylogenetic tree?

  if phylogenetic tree is drawn on software programme ,the sequence length changes the phylogeny .With the change in the sequence length ,there is again change in phylogenetic tree.Then is it so thatif phylogenetic tree is drawn on software programme ,the sequence length changes the phylogeny .With the change in the sequence length ,there is again change in phylogenetic tree.Then is it so that the phylogenetic tree is considered only for the given sequence only and not the entire gene sequence?

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  • 
    Sanjay Singh replied

    Phylogenetic Analysis is completly depends on the Alignment of the sequences..One can draw the phylogenetic tree with very short sequences also but the alignment of the sequences should be proper.IfPhylogenetic Analysis is completly depends on the Alignment of the sequences..One can draw the phylogenetic tree with very short sequences also but the alignment of the sequences should be proper.If the DNA sequence is small the porbability of the wrong alignment is more..So with the correct alignment you will always get the same phylogenetic tree..irrespective to the software..Phylogenetic position in the tree will be the same..

    Jun 3, 2011

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  • 
    he Kai replied

    try to search what murphy did in mammals. for example : Using genomic data to unravel the root of the placental mammal phylogeny

    Nov 28, 2010
• Steffen Kiel

  saving PAUP consensus trees

  Hi, does anyone know how to save a strict consensus and a 50% majority rule tree in PAUP?

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    Steffen Kiel replied

    Thanks Leticia - it works! In fact, if you write "strict=yes majrule=yes..." PAUP saves both trees in one file. Cheers, Steffen

    Apr 27, 2010

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