molecular-evolution
There are 56 repositories under molecular-evolution topic.
lukasturcani/stk
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
FePhyFoFum/phyx
phylogenetics tools for linux (and other mostly posix compliant) computers
chasewnelson/SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
cogent3/cogent3
Comparative Genomics Toolkit 3
LKremer/CAFE_fig
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
moshi4/MGCplotter
Microbial Genome Circular plotting tool for comparative genomics using Circos
jbpease/dfoil
DFOIL: Introgression Testing for Five Taxa
moshi4/CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
FePhyFoFum/PyPHLAWD
Python version of PHLAWD
laelbarlow/amoebae
Workflow for identifying and classifying homologous gene/protein sequences
LKremer/MSA_trimmer
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
jbloomlab/phydms
phylogenetic analyses informed by deep mutational scanning data
moshi4/FastDTLmapper
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
chasewnelson/OLGenie
Program for estimating dN/dS in overlapping genes (OLGs)
sishuowang/Solutions_Manual_CME2006_MESA2014
A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
almeidasilvaf/doubletrouble
An R package to identify and classify duplicated genes from whole-genome protein sequence data
jananiravi/compbio-gists
Computational Biology & Bioinformatics Resources
jbpease/mvftools
Multisample Variant Format ToolKit
wudangt/awesome-molecular-modeling-and-drug-discovery
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
chasewnelson/trevolver
Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context
V-Z/course-r-mol-data
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
louisgt/SodaPop
A tool for multiscale forward-time simulation of protein evolution.
wesleybeckner/gains
project that enables molecular design and computational screening of small molecules
Smithsonian/Fabaceae_Phylogenomics_workflow
Target-enrichment data processing in legumes
for-giobbe/BASE
Pronunced /'baze/ - is a tool which allows to integrate non-ubiquitous genes in comparative genomics analyses for selection.
JAlvarezJarreta/MEvoLib
Molecular Evolution Library for Python
RichardAGoldstein/HaROLD
Haplotype RecOnstruction using Longitudinal sequencing Data
jamesjcai/MBEToolbox
MBEToolbox: Matlab toolbox for molecular evolution
chenyangkang/Fasta2Codeml
A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.
gawbul/gawbul.github.io
Homepage of Dr Stephen P. Moss, Computational Scientist
j3551ca/BEAST-FLOW
Nextflow pipeline for estimation of evolutionary rate using Bayesian statistics.
jmenglund/predsim
Simulate predictive datasets from MrBayes' output
JRaviLab/MolEvolvR
An R Package for characterizing proteins using molecular evolution and phylogeny
radamsRHA/SpeciesTopoTestR
SpeciesTopoTestR: Likelihood-based hypothesis tests of species topologies in R
sennettm/Extant_Sequence_Reconstruction_ESR
Calculate conditional probability distributions of extant sequences given a phylogenetic tree, sequence alignment, and evolutionary model.