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03/26/15: BAli-Phy 2.3.6 released. Fix bugs, add M3 model ( more news. 08/26/14: BAli-Phy used for large 117-taxon tree. By McKenzie et. al. 05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Is MCMC software developed by Ben Redelings. For simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling. Works on the nucleotide, amino acid, and codon levels and can utilize complex substitution m...

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BAli-Phy: Welcome! | bali-phy.org Reviews

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03/26/15: BAli-Phy 2.3.6 released. Fix bugs, add M3 model ( more news. 08/26/14: BAli-Phy used for large 117-taxon tree. By McKenzie et. al. 05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Is MCMC software developed by Ben Redelings. For simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling. Works on the nucleotide, amino acid, and codon levels and can utilize complex substitution m...

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BAli-Phy: Welcome! | bali-phy.org Reviews

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03/26/15: BAli-Phy 2.3.6 released. Fix bugs, add M3 model ( more news. 08/26/14: BAli-Phy used for large 117-taxon tree. By McKenzie et. al. 05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Is MCMC software developed by Ben Redelings. For simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling. Works on the nucleotide, amino acid, and codon levels and can utilize complex substitution m...

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bali-phy.org

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BAli-Phy: Welcome!

http://www.bali-phy.org/index.php

Release 2.3 *. 01/30/16: BAli-Phy 2.3.8 released. Speed improvements ( more news. 08/26/14: BAli-Phy used for large 117-taxon tree. By McKenzie et. al. 05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Is MCMC software developed by Ben Redelings. For simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling. Works on the nucleotide, amino acid, and codon levels and can utilize complex sub...

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BAli-Phy: Graphical Models

http://www.bali-phy.org/models.php

BAli-Phy: Software for Bayesian Estimation of Alignment and Phylogeny. Release 2.3 *. BAli-Phy has been extended to express generic models written as graphical models. This is similar to other projects, such as RevBayes. These projects use languages like XML or R. To flexibly express generic models, and to construct models in a modular fashion [ 1. BAli-Phy currently does inference using MCMC. We have not yet added any support for SMC. BAli-Phy attempts to extend this paradigm by implementing. We can als...

3

BAli-Phy: Download

http://www.bali-phy.org/download.php

BAli-Phy: Software for Bayesian Estimation of Alignment and Phylogeny. Release 2.3 *. Please follow the installation instructions in the Manual. Linux (64-bit): Intel (26M). Mac OS (10.9 and up). You can use homebrew. To install bali-phy from homebrew/science. Requires XCode 5 compiler. 32-bit MinGW: Intel (34M). 64-bit MinGW: Intel (34M). On Windows. To see the requirements in detail, view the section in the User's Guide. Benjamin . redelings * gmail com.

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BAli-Phy: Examples

http://www.bali-phy.org/examples.php

BAli-Phy: Software for Bayesian Estimation of Alignment and Phylogeny. Release 2.3 *. Example analyses with results. 5S rRNA - 25 sequences. 5S rRNA - 48 sequences. Globins - 28 sequences. Transcribed Spacers 5.8S - 68 sequences. Bali-phy -c 8.script. Benjamin . redelings * gmail com.

5

BAli-Phy Tutorial

http://www.bali-phy.org/Tutorial2.html

2 Setting up the. 3 Command line options. 41 Inspecting output files. 42 Summarizing the output. 43 Generating an HTML Report. 5 Starting and stopping the program. 61 A simple multi-gene analysis. 62 Using different models in different partitions. 63 Using different indel models models. 64 Sharing model parameter between partitions. 65 Sharing substitution rates between partitions. 81 Splitting and Merging Alignments. 82 Shrinking the data set. 83 Cleaning the data set. 2 Setting up the. This is just 50 ...

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Benjamin Redelings: Evolution, Computation, Statistics

http://www.ben-redelings.org/index.html

Evolution, Computation, Statistics. Feb 2017: OpenTree manuscript accepted in PeerJ. A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species" [ Preprint v1. Jun 2016: Presentation at Evolution 2016 meeting in Austin, TX. New methods for constructing the supertree of life". Jan 2016: BAli-Phy 2.3.8. Nov 2015: Manuscript published in Genetics. A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation." [ PDF. On the Open Tree of Life. Evolutio...

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BAli-Phy: Welcome!

03/26/15: BAli-Phy 2.3.6 released. Fix bugs, add M3 model ( more news. 08/26/14: BAli-Phy used for large 117-taxon tree. By McKenzie et. al. 05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Is MCMC software developed by Ben Redelings. For simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling. Works on the nucleotide, amino acid, and codon levels and can utilize complex substitution m...

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