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This repository includes a compressed archive with supplementary files generated for the Thesis written in partial fulfillment of the requirements for the Master of Science (OEP-Biology).
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FOGS / fogs_portal_indexer
MIT LicenseUpdated -
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FOGS / fogs_snpstr_import
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BioCASe / VCAT-Transfer
GNU General Public License v2.0 or laterUpdated -
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This is a fork that only includes the script to choose the optimal annotated transcriptome after gene orthology inference with Orthograph.
ortho-overlap.py is being updated to work with the results from BUSCO as well.
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ZFMK / ZFMKDigitizationStrategy
Creative Commons Attribution Share Alike 4.0 InternationalUpdated -
Filtering a multiple sequence alignment excluding positions where a taxa group is the only representative.
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A template to structure data, code and documentation for a project on the HPC-Cluster
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Endpoint for getting ASV taxonomy tables as BIOM JSON files. http://gensoft.pasteur.fr/docs/biom-format/2.1.5/index.html
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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.
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BioCASe / biocase_media
GNU General Public License v2.0 or laterZFMK's virtual collection catalogue transfer and dissemination package
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