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--- multi-gene_phylogeny_pipeline [2018/02/05 12:04] – 129.173.88.82
+++ multi-gene_phylogeny_pipeline [2018/03/10 11:07] (current) – 173.212.69.201
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 Documentation by Kate Glennon, Sarah Shah, Shelby Williams, and Tommy Harding.
-The **Bordor** dataset is a set of 351 housekeeping genes that are well-conserved across all eukaryotes. This pipeline uses the gene sequences from //Arabidopsis thaliana// as queries to fish for homologues during the BLAST step.
+The **Bordor** dataset is a set of 351 housekeeping genes that are well-conserved across all eukaryotes. This pipeline uses the gene sequences from //Arabidopsis thaliana// as queries to fish for homologues during the BLAST step. Credit goes to Matt Brown & co.: [[https://doi.org/10.1093/gbe/evy014]], [[https://doi.org/10.1093/molbev/msx162]]
 All the original transcriptom/proteome files that are in the Bordor alignment is in **/scratch2/mbrown/PhylogenomicDatabases**
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 This will sequentially add the appropriate sequences for all the organisms of interest to the Bordor dataset. Trimming will not occur until the last taxon is added.
+NOTE2: If you have alignment files from someone else, and you want to add your own transcriptomes to them, move the alignment files in the folder "old_aln" in your START folder.
 Step 4: If everything went as expected, there will be a folder named “bmge_trimmed_old” in the “END*” folder. Download a bunch of *.faa (aligned non-trimmed sequences) and *.bmge.fas (trimmed aligned sequences) files to your computer and examine them with a sequence viewer such as AliView. The last line(s) is the sequence from your transcriptome/protein data that was aligned to the other sequences of that particular gene. Make sure they look aligned; for instance, if all other sequences have a “GGG” in a specific location then you should expect your sequence to have the same. The .bmge.fas files are .faa files in which the badly-aligned positions were trimmed away.