species-tree

There are 0 repository under species-tree topic.

• dongwei1220 / EasySpeciesTree

  Easily construct the ML species tree with single-copy gene shared by different species.

  species-treeshellpython
  Language:Python 25

• reslp / phylociraptor

  rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

  bioinformaticsgenomicsphylogeneticspipelinephylogenomicsphylogenomics-pipelinesnakemakespecies-treemaximum-likelihood
  Language:Python 23

• tomas-fer / HybPhyloMaker

  Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees)

  hybseq-dataspecies-treephylogenomics-pipelinelocus-selection
  Language:Shell 19

• Mahim1997 / wQFM-2020

  wQFM implementation in Java

  bioinformaticsphylogeneticsweighted-quartetsspecies-treegene-treejavapythonperlbash-scriptdendropyphylonet
  Language:Perl 15

• V-Z / hybseq-scripts

  Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

  ngs-pipelinehybseq-dataphylogenomicsngsdata-sciencedata-analysismolecular-biologyparalogsbioinformatics-pipelinebioinformatics-scriptsbioinformatics-analysisgenomicsbioinformaticshybpipergene-treealignmentsspecies-treehybseq-scriptsmetacentrumngs-scripts
  Language:Shell 4

• islamazhar / STELAR

  Dynamic Programming (DP) based software Software to Estimate Species Tree by maximizing triplet agreement.

  phylogeneticsphylogenetic-treestripletsspecies-treegene-trees
  Language:Python 3

• niconm89 / BUSCO2Tree

  This pipeline helps to build a phylogenetic tree using the BUSCO results over a group of species/genomes/proteomes/transcriptomes.

  bioinformaticsbuscogenomicsphylogenomicsphylogenomics-pipelinepythonspecies-treecompleteness
  Language:Python 2

• juliawiggeshoff / astral-species-tree

  This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 bootstrap replicates for each tree. Then, consensus trees are produced and combined to infer a species tree following the multispecies coalescent model with ASTRAL. Imported from my GitLab.

  astralmultispecies-coalescentsnakemakespecies-treeworkflowiq-treemaximum-likelihood
  Language:Python 0