Leo Martins

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

Software and code

Tatajuba

Identification and classification of homopolymeric tracts from reads

source code on github

Uvaia

Reference-based alignment and search against aligned database

source code on github

Super Distance

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

source code on github

Peroba

Phylogenetic exploration of SARS-CoV-2 sequences

source code on github

Guenomu

Hierarchical Bayesian species tree estimation from multi-gene family data

source code on bitbucket

Genefam-dist

Signature inference of gene family trees from anchoring species trees.

source code on github

SpecImage

Python module to work with hyperspectral imaging data.

source code on github

biomcmc-lib library

C library with low level functions for phylogenetic analyses

source code on github

Recomb-biomc2

Hiearchical Bayesian Model for Viral Phylogenetic Recombination

source code on github

Cumaru

(Experimental) multiple sequence alignment based on kalign3

source code on github

Curupixa

(Experimental) thread-safe API-aware C library to supercede biomcmc-lib someday

source code on github

Supplementary analyses for manuscripts

Salmonella Biofilm

Jupyter notebooks with analyses of experimental evolution of Salmonella biofilms

github repository

rRNA phylogenetics

Analysis of the phylogenetic resolution of the rRNA operon

github repository

Tree homology tests

Critical evaluation of tree-based homology inference

bitbucket repository

Documentation and Texts

Binfie notes

Blog with technical notes on bioinformatics algorithms and implementations

Notebooks webpage

biomcmc-lib API

Doxygen documentation for employing biomcmc-lib source code

API documentation page

bioMCMC blog

Old blog with phylogenetics observations and new papers

read blog posts

Mastodon