Questions tagged [beast]

Phylogenetics package based on Bayesian statistics often used in molecular clock calculation

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Estimating rate of evolution from a phylogeny

Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species? I was using terminal branch length from a phylogeny and would quite like to try sub ...
Nitara Wijayatilake's user avatar
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1 answer
108 views

How to parallelize BEAST

I'm running BEAST v1.10.4 with BEAGLE v4.0.0. My dataset has one large partition and I have access to a machine with many CPUs so I would like to optimize performance by parallelizing the process. ...
flaszlok's user avatar
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3 votes
1 answer
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What is the limit of partition incompleteness in Bayesian MCMC?

I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis. I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in ...
Vovin's user avatar
  • 435
3 votes
1 answer
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What is & how to solve File error: my.xml.state (Remote I/O error)?

I caught the next exception during my phylogeographical analysis in BEAST 2 with GEO_SPHERE. What could be the reason? & how to evade this in the future? ...
Vovin's user avatar
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4 votes
2 answers
237 views

What can be the reason of getting negative branches lengths after BEAST analysis?

BEAST2 is currently being used for tree reconstruction prior phylogeographic analysis. The sample size and loci are described below. I thought that BEAST/BEAST2 does not allow negative lengths of ...
Vovin's user avatar
  • 435
3 votes
1 answer
106 views

Missing ',' in line when Biopython reads a nexus tree

I want to edit a tree that I got from BEAST2 treeannotator in nexus-format. Usually I use the module Phylo from Biopython for such work but ...
Vovin's user avatar
  • 435
0 votes
1 answer
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BEAGLE do not see and/or not use OpenCL

I am conducting phylogeny analyses using BEAST 2 as software tool. It is said that it can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS. I ...
Vovin's user avatar
  • 435
-1 votes
2 answers
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How to use GEO_SPHERE?

I have some problems with geosphere package which extends/applies the Beast Bayesian MCMC package for calculating phylogenetic trees. Please, could anyone give any hints about at least one of them? ...
Vovin's user avatar
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1 vote
1 answer
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BEAUti not accepting taxa tip dates

I'm using BEAUti as part of my pipeline and the sequence names include | to separate the metadata fields - with culture date being at the very end. When I attempt ...
MicroBiostat's user avatar
4 votes
1 answer
195 views

Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
JaydenM-C's user avatar
  • 149
5 votes
2 answers
286 views

Calculate the percentage of each unique phylogenetic tree in a BEAST output

I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output? I already ...
jvddorpe's user avatar
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