phylogenomics-pipeline

There are 0 repository under phylogenomics-pipeline topic.

• vinuesa / get_phylomarkers

  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

  phylogenomicspopulation-geneticsphylogenomics-pipelinespecies-treesmarkersgenomicspipelinephylogeneticsphylogenetic-treescodon-alignmentmaximum-likelihoodorthologuesspecies-delimitationmicrobiologycore-genomeperlrbashclock-hypothesisrecombination
  Language:Perl 47

• 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 18

• V-Z / sondovac

  Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

  sciencephylogeneticsngs-pipelinengs-analysisngsgeneticsmolecular-biologyphylogenomics-pipelinephylogenomicspipelinehybseq-dataorthologuestranscriptomedata-analysisdata-sciencephylogenomictaxonomic-classificationbioinformaticsbioinformatics-pipelinebioinformatics-analysis
  Language:TeX 5

• AKU-CITRIC-Center-for-Bioinformatics / ncov

  Genomic Epidemiology of SARS-CoV-2 in Pakistan

  githubnextflowyamlgenomicsepidemiologygenomics-visualizationepidemiology-analysisepidemiology-modelspyhylodynamicsphylogeneticsphylosurveillancephylogenomicsphylogenetic-analysisphylogenetic-dataphylogenetic-treesphylogeographyphylogenomics-pipeline
  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

• Public-Health-Bioinformatics / irida-plugin-snippy-phylogenomics

  Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

  irida-pipelinebioinformatics-pipelinephylogenomics-pipelinemicrobial-genomics
  Language:Java 2

• guyleonard / orchard

  :seedling: :clipboard: :arrow_right: :8ball: :arrow_right: :palm_tree: :evergreen_tree: :deciduous_tree: - A quick phylogenetic tree building pipeline!

  phylogenomicsphylogenomics-pipelinephylogenetic-trees
  Language:Perl 1

• schultzm / havic

  Detect Hepatitis A Virus Infection Clusters

  viral-genomicstransmissioncluster-analysisphylogenomics-pipeline
  Language:Python 1

• gsgarlata / Eliurus-Phylogenomics

  This repository includes scripts and data used in Sgarlata et al., 2023 entitled "The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species".

  phylogenomics-pipelinerad-seqspecies-delimitationspatial-phylogenomics
  Language:PostScript 0

• pendy05 / MISPhyl

  Mutual Information Supermatrix Phylogenomics Pipeline (MISPhyl): Reconstructs Phylogenomics Tree based on Mutual Information Evaluated Phylogenetics Signals From Genomes Derived Orthologous Sets

  mutual-informationphylogenomics-pipelinepython
  Language:Python 0