Phylogenetic orthology inference for comparative genomics
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Oct 22, 2024 - Python
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gene-trees
Here are 16 public repositories matching this topic...
TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
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Oct 9, 2019 - C
NGSphy: phylogenomic simulation of next-generation sequencing data
coverage next-generation-sequencing read-counts phylogenomics species-trees gene-trees targeted-sequencing
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Mar 9, 2018 - Python
A tool for divide-and-conquer tree estimation via a shared distance matrix
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Mar 19, 2019 - Python
Species tree estimation from gene trees via weighted quartets
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Apr 27, 2025 - C++
Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)
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Jan 4, 2021 - Shell
Species tree estimation from multi-copy gene trees
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Oct 13, 2021 - Python
Coalescent-Aware Species Tree Length Estimation in Substitution-units
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Oct 17, 2024 - Mathematica
Genetic Algorithm for gene Tree Construction/Correction optimal under sequence likelihood and reconciliation score
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Mar 2, 2019 - C
Dynamic Programming (DP) based software Software to Estimate Species Tree by maximizing triplet agreement.
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May 27, 2020 - Python
Rooting species trees under the multi-species coalescent model
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Jul 11, 2023 - Python
Implementation of the Super-Reconciliation model for reconciling a set of trees accounting for segmental duplications and losses.
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Aug 28, 2018 - C++
Datasets and scripts for "Coalescent-based branch length estimation improves dating of species trees" paper
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Apr 23, 2025 - R
Species tree estimation from gene trees via quartets
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Mar 21, 2024 - C++
AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees
tree gene detection pool ast selection sampling sequence trees linux-os gene-trees phylogeneitc horizontal-gene-transfers
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May 24, 2017
Compresses SimPhy datasets into a single gzipped file for all the gene trees and gzipped mulitple sequence alignments for all the loci.
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Apr 4, 2018 - Python
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