Difference between revisions of "BALi-Phy"

Revision as of 16:08, 27 May 2022

Description

BAli-phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.

BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

Required Modules

Serial

gcc/5.2.0
bali-phy

Example:

module load gcc/5.2.0 bali-phy

System Variables

HPC_BALI-PHY_DIR - installation directory
HPC_BALI-PHY_BIN - executable program directory
HPC_BALI-PHY_LIB - library directory

Citation

- Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny, Systematic Biology, 54(3):401-418, 2005 [PDF]

- Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. [PDF]

- Redelings BD and Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7:40, 2007. [PDF]

- Redelings BD. Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Mol. Biol. Evo. 31(8), 2014. [WWW]

@@ Line 1: / Line 1: @@
 [[Category:Software]][[Category:Biology]]
 {|<!--CONFIGURATION: REQUIRED-->
-|{{#vardefine:app|BALi-Phy}}
+|{{#vardefine:app|BAli-phy}}
-|{{#vardefine:url| http://loco.biosci.arizona.edu/bali-phy/}}
+|{{#vardefine:url|http://www.bali-phy.org/}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
 |{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
+|{{#vardefine:slurm|}}            <!--SLURM SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 18: / Line 19: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-BAli-Phy is software by Ben Redelings that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. It uses likelihood-based evolutionary models of substitutions and insertions and deletions to place gaps. It has been used in published analyses on data sets up to 117 taxa.
+'''BAli-phy''' is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.
+BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.
 <!--Modules-->
-==Environment Modules==
+==Required Modules==
-Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+===Serial===
+* gcc/5.2.0
+* bali-phy
+Example:
+ module load gcc/5.2.0 bali-phy
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
+* HPC_{{uc:{{#var:app}}}}_LIB - library directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 31: / Line 43: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
 WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+|}}
+<!--PBS scripts-->
+{{#if: {{#var: pbs}}|==PBS Script Examples==
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
+|}}
+<!--SLURM scripts-->
+{{#if: {{#var: slurm}}|==SLURM Script Examples==
+See the [[{{PAGENAME}}_SLURM]] page for {{#var: app}} SLURM script examples.
 |}}
-<!--Job Scripts-->
-{{#if: {{#var: job}}|==Job Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
-|}}
 <!--Policy-->
 {{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (Licensing, usage, access).
 |}}
 <!--Performance-->
 {{#if: {{#var: testing}}|==Performance==
 WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 |}}
 <!--Faq-->
@@ Line 56: / Line 68: @@
 <!--Citation-->
 {{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{#var:app}} you have to cite it as follows:
+- Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny, Systematic Biology, 54(3):401-418, 2005    [PDF]
+- Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006.     [PDF]
+- Redelings BD and Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7:40, 2007.    [PDF]
-WRITE_CITATION_HERE
+- Redelings BD. Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Mol. Biol. Evo. 31(8), 2014. [WWW]
 |}}