Beast code in Giters

pegi3s's repositories

dockerfiles

This repository contains Docker files for the images maintained by the Phenotypic Evolution Group at the Institute for Molecular and Cell Biology / Instituto de Investigação e Inovação em Saúde da Universidade do Porto.

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phylogenetic-tree-collapser

Phylogenetic Tree Collapser

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orthologs-finder

Commands to retrieve orthologous genes from DIOPT or Ensembl.

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pss-fs

FastScreen: a Compi pipeline for Fast Screening of PSS (Positively Selected Sites).

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pss-genome-fs

GenomeFastScreen: a Compi pipeline for Fast Screening of PSS (Positively Selected Sites).

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two-way-blast

A Compi pipeline for finding orthologs using a two-way BLAST approach.

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auto-phylo

A Docker-based pipeline maker for phylogenetic studies

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auto-pss-genome

Auto-PSS-Genome (Automatic Positively Selected Sites Genome) is a Compi pipeline to automatically identify positively selected amino acid sites using three different methods, namely CodeML, omegaMap, and FUBAR in complete genomes (FASTA files containing all coding sequences).

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cga

CGA (Conserved Genome Annotation) is a Compi pipeline to efficiently perform CDS annotations by automating the steps that researchers usually follow when performing manual annotations.

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check-cds

CheckCDS: a compi pipeline to produce valid CDS files.

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classify

Image classification using PyTorch

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evoppi-querier

A program to make queries to the EvoPPI web server.

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haddock-tools

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ipssa

IPSSA (Integrated Positively Selected Sites Analyses): a Compi pipeline for to automatically identify positively selected amino acid sites using CodeML, omegaMap, and FUBAR.

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