Loading debian/tests/data/READMEdeleted 100644 → 0 +0 −14 Original line number Diff line number Diff line In order to get a FASTA file from all the Skunavirus genomes, the NCBI database was used: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Skunavirus,%20taxid:1623305 Select Download, Select Data Type (Sequence Data/FASTA Format) The rest of the data is generated with this workflow in mind: 1. Using the package prodigal to generate a database file 2. Using awk to filter this 3. Using mcl to generate protein families 4. Using a custom python script to do pairwise comparisons 5. Out of the files generated in the previous step, I am using mcl again to build clusters of genomes. You can find more details inside the LMCLUST.sh Loading
debian/tests/data/READMEdeleted 100644 → 0 +0 −14 Original line number Diff line number Diff line In order to get a FASTA file from all the Skunavirus genomes, the NCBI database was used: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Skunavirus,%20taxid:1623305 Select Download, Select Data Type (Sequence Data/FASTA Format) The rest of the data is generated with this workflow in mind: 1. Using the package prodigal to generate a database file 2. Using awk to filter this 3. Using mcl to generate protein families 4. Using a custom python script to do pairwise comparisons 5. Out of the files generated in the previous step, I am using mcl again to build clusters of genomes. You can find more details inside the LMCLUST.sh