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ZFMK's virtual collection catalogue transfer and dissemination package
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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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This is a fork with the necessary tools to generate reference FASTA files on the protein and gene levels and a modified orthology table, all of which are compatible with and necessary to annotate orthologs with Orthograph v0.6.3. Created to fix incompatibility issues between the information stored in the catalog from OrthoDB v10.1 and the protein ID's in the sequence headers from the RefSeq files from NCBI.
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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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Filtering a multiple sequence alignment excluding positions where a taxa group is the only representative.
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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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