Explore projects
-
BioCASe / biocase_media
GNU General Public License v2.0 or laterZFMK's virtual collection catalogue transfer and dissemination package
Updated -
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.
Updated -
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.
Updated -
Forked repo used to filter the results generated with checker_complete.2.pl, which finds outlier sequences in multiple sequence alignments on the amino acid level.
To be modified: several of the scripts are tailored to sequence headers labeled with AD followed by numbers ranging from 0 to 9, repeating it 2 times and a maximum of 3 times. Likewise, it searches for orthologous groups from OrthoDB v10.1, which always include "at6447" in their identifier. Additionally, to remove the outliers some scripts parse the FASTA files with the suffix .aa.mafft.fas.
Updated -
Updated
-
A template to structure data, code and documentation for a project on the HPC-Cluster
Updated -
Endpoint for getting ASV taxonomy tables as BIOM JSON files. http://gensoft.pasteur.fr/docs/biom-format/2.1.5/index.html
Updated