Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs
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Sep 18, 2019 - Python
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orthofinder
Here are 10 public repositories matching this topic...
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
python bioinformatics evolution gene-expression transcriptome gene-expression-profiles orthofinder tai scrna-seq-analysis phylostratigraphy scanpy expression-profiles orthomap
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Nov 20, 2023 - Python
scTEI - add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects
bioinformatics evolution gene-expression gene-expression-profiles orthofinder seurat scrna-seq-analysis phylostratigraphy expression-profiles seurat-objects sctei
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May 17, 2025 - HTML
A set of scripts for running a CAFE5 gene family evolution analysis, from OrthoFinder's output.
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May 11, 2026 - Shell
A pipeline to reconstruct a species tree with RaxML, from Single-Copy Orthologues (SCOs) identified by OrthoFinder.
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May 18, 2026 - Shell
Repository containing code I have written in R.
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Apr 7, 2023
Comparative phylogenetic inference in Capsicum: alignment-free MinHash distances vs. alignment-based transcriptome assemblies (course write-up, 2025)
bioinformatics rna-seq phylogenetics capsicum transcriptomics phylogenomics astral orthofinder sourmash iqtree
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Sep 2, 2026 - Shell
Scripts I wrote as a graduate research assistant while working on the Wyeomyia smithii Genome project for Dr. Elizabeth Cooper's Lab at UNC Charlotte
python bash r genome-annotation mosquito transposable-elements orthofinder hpc-cluster repeatmodeler clustalo ltrharvest itol
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Apr 16, 2024 - Python
Interactive phylogenetic gene-family gain/loss maps from OrthoFinder and PIRATE
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Aug 16, 2026 - HTML
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