{"id":72,"date":"2022-05-16T16:02:19","date_gmt":"2022-05-16T15:02:19","guid":{"rendered":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/?page_id=72"},"modified":"2022-05-17T17:28:44","modified_gmt":"2022-05-17T16:28:44","slug":"software","status":"publish","type":"page","link":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"

Bait-ER<\/a><\/h3>\n

A fully Bayesian approach to estimate selection coefficients from Evolve & Resequence time series data.<\/p>\n

Reference: Barata, Borges and Kosiol, Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments<\/em>, bioRxiv<\/em>, 2020, doi.org\/10.1101\/2020.12.15.422880<\/span><\/a><\/p>\n

 <\/p>\n

GPrank R package<\/a><\/h3>\n

R package for ranking genomic time series using Gaussian Process models. The package allows for finding potential selection targets in Evolve & Resequence experiments.<\/p>\n

References: Topa and Honkela, Analysis of differential splicing suggests different modes of short-term splicing regulation<\/em>, Bioinformatics, 2016, doi.org\/10.1093\/bioinformatics\/btw283<\/a><\/em><\/p>\n

Topa, Jonas, Kofler, Kosiol and Honkela, Gaussian process test for high-throughput sequencing time series: application to experimental evolution<\/em>, Bioinformatics<\/em>, 2015, doi.org\/10.1093\/bioinformatics\/btv014<\/a><\/p>\n

 <\/p>\n

IQ-TREE PoMo<\/a><\/h3>\n

Polymorphism-aware phylogenetic Models (PoMo) applied to phylogenetic tree inference using population data (site frequency data). One may reconstruct a maximum-likelihood tree from alignment data using IQ-TREE PoMo.<\/p>\n

Reference: Schrempf, Minh, De Maio, von Haeseler, and Kosiol, Reversible polymorphism-aware phylogenetic models and their application to tree inference<\/em>, Journal of Theoretical Biology<\/em>, 2016, doi.org\/10.1016\/j.jtbi.2016.07.042<\/a><\/p>\n

 <\/p>\n

RevBayes PoMo<\/a><\/h3>\n

The PoMo models’ full-likelihood approach also allows for Bayesian inference of species trees.<\/p>\n

Includes tutorials<\/a> on how to run PoMo on RevBayes.<\/p>\n

References: Borges, Boussau, Sz\u00f6ll\u0151si and Kosiol, Pervasive selection biases inferences of the species tree<\/em>, bioRxiv<\/em>, 2020, doi.org\/10.1101\/2020.07.30.228965 <\/span><\/a><\/span><\/p>\n

Borges, Sz\u00f6ll\u0151si and Kosiol, Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models<\/em>, Genetics<\/em>, 2019, doi.org\/10.1534\/genetics.119.302074<\/a><\/span><\/p>\n

 <\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

Bait-ER A fully Bayesian approach to estimate selection coefficients from Evolve & Resequence time series data. Reference: Barata, Borges and Kosiol, Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments, bioRxiv, 2020, doi.org\/10.1101\/2020.12.15.422880   GPrank R package R package for ranking genomic time series using Gaussian Process models. The package allows for…<\/p>\n","protected":false},"author":50,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-72","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages\/72","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/users\/50"}],"replies":[{"embeddable":true,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/comments?post=72"}],"version-history":[{"count":0,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages\/72\/revisions"}],"wp:attachment":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/media?parent=72"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}