Repositories list

• sowing

  Public
  Immutable tree data structure in Python, with utilities to build, traverse, edit, and serialize trees

  pythonimmutablephylogenetics+ 3zippertree-structuresupertree

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 8, 2025Feb 8, 2025

• superrec2

  Public
  Run and compare algorithms for phylogenetic reconciliation and super-reconciliation

  reconciliationphylogeneticssynteny+ 1maximum-parsimony

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Oct 17, 2024Oct 17, 2024

• CoreTracker

  Public
  CoreTracker, a codon reassignment tracker

  genetic-codemetazoacodons+ 3pythongenomecodon-reassignment

  Python

  •

  Other

  •3•5•1•2•Updated Jun 17, 2024Jun 17, 2024

• superrec-tutorial

  Public
  Perl

  •0•0•0•0•Updated Jul 4, 2023Jul 4, 2023

• GATC

  Public
  Genetic Algorithm for gene Tree Construction/Correction optimal under sequence likelihood and reconciliation score

  gene-treesgenetic-algorithm

  C

  •

  GNU General Public License v3.0

  •0•4•1•0•Updated Mar 2, 2019Mar 2, 2019

• EdChecker

  Public
  Computational methods for RNA editing sites prediction

  Python

  •0•0•0•0•Updated Sep 27, 2018Sep 27, 2018

• SuperReconciliation

  Public
  Implementation of the Super-Reconciliation model for reconciling a set of trees accounting for segmental duplications and losses.

  bioinformaticsreconciliationgene-trees+ 1segmental-duplications

  C++

  •1•2•0•0•Updated Aug 28, 2018Aug 28, 2018

• LabelGTC

  Public
  Implementation of LabelGTC algorithm

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 19, 2018Apr 19, 2018

• SuGeT

  Public
  SuperGeneTree maker

  C++

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 19, 2018Apr 19, 2018

• MiscTreeUtils

  Public
  Misc utils in python for phylogenetic analysis.

  Python

  •0•0•0•0•Updated Feb 1, 2018Feb 1, 2018

• profileNJ

  Public
  Genome evolution-aware gene trees correction without losing sequence information

  Python

  •

  GNU General Public License v3.0

  •2•3•1•1•Updated Jul 18, 2017Jul 18, 2017

• OrthoPara-ConstraintChecker

  Public
  A program to check if a given set of orthology/paralogy relations, with possible unknowns, is satisfiable or consistent with a species tree.

  Python

  •0•1•0•0•Updated Jun 13, 2016Jun 13, 2016

• paralogy-corrector

  Public
  C++

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 5, 2015Jan 5, 2015

• polytomy-solver-web

  Public
  Web application for various LBIT phylogenetic algorithms.

  Python

  •0•1•0•0•Updated Sep 3, 2014Sep 3, 2014

• polytomy-solver-distance

  Public
  C++

  •0•1•1•0•Updated Aug 28, 2014Aug 28, 2014