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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.

This forked repository includes a compressed archive with the supplementary files, as well as the Thesis written in partial fulfillment of the requirements for the Master of Science (OEP-Biology) from the University of Bonn, Germany. Published originally with my maiden name, Júlia M. Q. Calvet

Thesis title: Evaluation of de novo transcriptome assemblers and their performance when reconstructing single-copy orthologous genes: the effects of complete sets of data when establishing relationships between dorid nudibranchs

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.