Below you will find links to other pages with code, documentation, and technical notes for bioinformatics and computational evolutionary biology software.

Software and code

guenomu

Guenomu

Hierarchical Bayesian species tree estimation from multi-gene family data

source code on bitbucket

genefam_dist

Genefam-dist

Signature inference of gene family trees from anchoring species trees.

source code on github

specimage

SpecImage

Python module to work with hyperspectral imaging data.

source code on github

biomcmclib

biomcmc-lib library

C library with low level functions for phylogenetic analyses

source code on github

super_distance

Super Distance

Supertree estimation from gene family trees, using matrix representation with distances

source code on github

recomb-biomc2

Recomb-biomc2

Hiearchical Bayesian Model for Viral Phylogenetic Recombination

source code on github

peroba

Peroba

Phylogenetic exploration of SARS-CoV-2 sequences

source code on github

cumaru

Cumaru

(Experimental) multiple sequence alignment based on kalign3

source code on github

tatajuba

Tatajuba

(Experimental) identification and classification of homopolymeric tracts from reads

source code on github

uvaia

Uvaia

Reference-based alignment and search against aligned database

source code on github

Supplementary analyses for manuscripts

Salmonella biofilm

Salmonella Biofilm

Jupyter notebooks with analyses of experimental evolution of Salmonella biofilms

github repository

long-read rRNA phylogenetics

rRNA phylogenetics

Analysis of the phylogenetic resolution of the rRNA operon

github repository

UCA test bias

Tree homology tests

Critical evaluation of tree-based homology inference

bitbucket repository

Documentation and Texts

notebooks

Notebooks

Project with technical notes on bioinformatics algorithms and implementations

Notebooks webpage

biomcmc-libdocs

biomcmc-lib API

Doxygen documentation for employing biomcmc-lib source code

API documentation page

biomcmc-blog

bioMCMC blog

Old blog with phylogenetics observations and new papers

read blog posts