codeml

Here are 13 public repositories matching this topic...

robinvanderlee / positive-selection

Scripts and procedures for detecting positively selected genes and codons in primates

bioinformatics genomics genetics evolution computational-biology ensembl bioinformatics-pipeline comparative-genomics genomes genome-analysis sequence-alignment bioinformatics-analysis positive-selection bioinformatics-scripts immunity primates codeml

Updated Nov 14, 2020
Perl

LKremer / MSA_trimmer

Star

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

phylogenetics trimming codon-alignment molecular-evolution sequence-alignment trimmer codeml multiple-sequence-alignment aligned-regions paml msa-trimmer alignment-trimming cds-alignment

Updated Mar 18, 2019
Python

for-giobbe / BASE

Star

Pronunced /'baze/ - is a tool which allows to integrate non-ubiquitous genes in comparative genomics analyses for selection.

selection omega comparative-genomics molecular-evolution codeml dnds

Updated Oct 8, 2021
Shell

Arkadiy-Garber / ParaHunter

Star

Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs

duplicates codeml paml paralogs gene-paralogs

Updated Feb 28, 2023
Python

philippmuench / fastcodeml_docker

Star

fastcodeml inside a docker container

docker-container selection fastcodeml-docker fastcodeml codeml

Updated Nov 17, 2016
Groff

chenyangkang / Fasta2Codeml

Star

A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.

selection ecology molecular-evolution codeml natural-selection paml

Updated Dec 12, 2024
Python

philippmuench / selection_docker

Star

dN/dS calculation based on codeml, fastcodeml and slimcodeml

docker selection fastcodeml codeml slimcodeml

Updated Jun 19, 2017
C++

pegi3s / pss-fs

Star

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

pipeline positive-selection codeml fubar compi fasttree

Updated Sep 2, 2022
Shell

Ahemdgggi / FastCode

Star

⚡ Boost code analysis and comprehension with FastCode, delivering fast, scalable, and cost-efficient solutions for Python projects.

python data-science communication exploratory-data-analysis codeigniter transformers efficient inference x86 meetups hedgefund codeml autocode fastcode javacode flash-attention

Updated Oct 12, 2026
Python

sing-group / adops

Star

Automatic Detection of Positively Selected Sites

java phylogenetic-trees phylogenetics fasta positive-selection mrbayes codeml biooinformatics java-bioinformatics

Updated Mar 13, 2019
Java

Vianpyro / CodeML-2025

Sponsor

Star

Voir les branches pour les differentes IA

python machine-learning hackathon codeml

Updated Oct 12, 2025
Dockerfile

Jari-van-Diermen / Spiny_mice_manuscript

Star

Pipeline for running the Acomys cahirinus positive selection analysis using HyPhy aBSREL, HyPhy MEME and PAML codeml

shell docker r meme singularity hyphy codeml pyt paml evolutionary-genomics absrel

Updated May 13, 2025
R

CodeMLYummy / optiframe

Star

OptiFrame: recycled lens photo to 3D-printed frame (CodeML 2026, SN-SF)

Updated Oct 11, 2026
Python

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