Streamlining phylogenomic data gathering, processing and visualization
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Sep 26, 2018 - Python
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orthologues
Here are 8 public repositories matching this topic...
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
bash r pipeline genomics perl phylogenetic-trees phylogenetics markers orthologues microbiology population-genetics codon-alignment maximum-likelihood phylogenomics species-trees recombination core-genome species-delimitation phylogenomics-pipeline clock-hypothesis
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May 7, 2026 - Perl
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
python shell bash data-science bioinformatics genetics biology ftp sge phylogenetics blast orthologues qsub orthology-inference ncbi sequence-alignment pbs orthologs orthology biosql
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Sep 6, 2026 - Python
A couple of tools I find indispensable for post orthomcl down-stream analysis.
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Oct 2, 2019 - Perl
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".
science data-science bioinformatics pipeline genetics ngs bioinformatics-pipeline phylogenetics data-analysis orthologues phylogenomic transcriptome phylogenomics molecular-biology bioinformatics-analysis ngs-analysis taxonomic-classification phylogenomics-pipeline ngs-pipeline hybseq-data
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Feb 16, 2024 - TeX
Find two-boxes transcription factor binding sites (made for sigma factor binding sites) by comparing intergenic DNA regions upstream pairs of orthologous genes using statistical analyses
statistics prediction orthologues promoter transcription-factor-binding-site sigma-factor-binding-site dna-motifs rmes sigffrid bmc-bioinformatics two-box-motifs
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Oct 6, 2020 - Perl
The local version of the RecBlast
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Mar 4, 2017 - Python
Phylogenetic tree of LAR and other PIP family enzymes as shown in Güngör et al. 2020. This repository details all code and intermediate files used.
biology open-data open-science orthologues phylogeny science-research protein-evolution open-notebook plant-genetic-resources plant-genomics
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Oct 6, 2020 - Jupyter Notebook
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