Project on Amine Receptor Phylogeny
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Manuscript
analysis
scripts
.gitignore
README.md

README.md

amine_receptors

This repository accompanies the paper Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors, by Spielman SJ, Kumar K, and Wilke CO. Contact Stephanie at stephanie.spielman@gmail.com with any questions.

Quick links!

  1. Structurally-informed, unmasked protein MSA and nucleotide MSA, both in FASTA format.

  2. Structurally-informed, masked protein MSA and nucleotide MSA, both in FASTA format.

  3. ML partitioned-phylogeny created with structurally-informed masked alignment, in newick format with branch lengths and bootstrap support included.

  4. Description of all sequences in final structurally-informed alignment. This is a tab-delimited file containing the ProteinID/NucleotideID, gene, and taxonomy.

  5. Alignments and phylogenies for each primary biogenic amine receptors subclade. Created from the masked structurally-informed MSA and its corresponding partitioned ML phylogeny.

Description of Contents

analysis/

  • Contains data (incl. sequences, alignments, phylogenies, sequence descriptions) used and generated during analysis pipeline. See README within for details.

scripts/

  • Contains all code used during analysis pipeline. See README within for details.

Manuscript/

  • Contains manuscript, figures, tables.