Multiple Alignments

HSPB8 (human): Blast results

Clustal Omega output: clustalo-I20161205-104802-0953-69402493-oy

Fasta header reformatting:

perl -p -i -e 's/>.+\[(.+) (.+)\]/>${1}_${2}/' ~/Downloads/sequence.fasta
More info on Perl One-liners.

WebSite with several tools for MSA: http://www.ebi.ac.uk/Tools/msa/

92 protein sequences with entry name starting with '5HT': uniprot_5HT.fasta.txt

For later: 5HT_kalign_tree.txt

Phylogenetic Trees

Some useful background information on phylogenetic trees:
  1. Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups
  2. Trait Evolution on a Phylogenetic Tree: Relatedness, Similarity, and the Myth of Evolutionary Advancement
  3. Examples of phylogenetic trees (based on Rhodopsin):