Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phylogenies/phylobayes33_wrapper.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 <tool id="phylobayes" name="Phylobayes" version="1.0"> | |
2 <description>version 3.3b</description> | |
3 <requirements> | |
4 <requirement type="binary">Phylobayes 3.3b</requirement> | |
5 </requirements> | |
6 <command interpreter="perl"> | |
7 phylobayes33_wrapper.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval | |
8 </command> | |
9 <inputs> | |
10 <param name="filename" type="data" format="txt" label="Input file (ali)" /> | |
11 <param name="nchain" type="integer" value="0" label="Number of chains to run" /> | |
12 <param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" /> | |
13 <param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" /> | |
14 <param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/> | |
15 <param name="burnin" type="integer" value="0" label="Post analysis burnin" /> | |
16 <param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/> | |
17 </inputs> | |
18 <outputs> | |
19 <data from_work_dir="dataset.con.tre" name="contre" format="txt" /> | |
20 <data from_work_dir="dataset.bplist" name="bplist" format="txt" /> | |
21 </outputs> | |
22 | |
23 <help> | |
24 | |
25 **How it works** | |
26 PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. | |
27 Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. | |
28 It is particularly well suited for large multigene alignments, such as those used in phylogenomics. | |
29 | |
30 The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests, | |
31 data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm. | |
32 | |
33 http://www.atgc-montpellier.fr/phylobayes/ | |
34 | |
35 **Citations** | |
36 Phylobayes - Bayesian phylogenetic software based on mixture models. | |
37 | |
38 Lartillot N., Philippe H. "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process." Molecular Biology and Evolution. 2004 21(6):1095-1109. | |
39 http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf | |
40 | |
41 Lartillot N., Philippe H. "Computing Bayes factors using thermodynamic integration." Systematic Biology. 2006 55:195-207. | |
42 http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf | |
43 | |
44 Lartillot N., Brinkmann H., Philippe H. "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model." BMC Evolutionary Biology. 2007 Feb 8;7 | |
45 Suppl 1:S4. | |
46 | |
47 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. | |
48 | |
49 Current Osiris Citation is here | |
50 | |
51 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
52 </help> | |
53 </tool> |