acorg / seqdb-make-tree-signature-page

Set of tools to build, query sequence database and to generate phylogenetic trees.

OBSOLETE!

use acorg/seqdb and acorg/signature-page

seqdb-make-tree-signature-page

Set of tools to build, query sequence database and to generate phylogenetic trees and signature pages. To be split into separate packages.

Requirements:

• macOS: clang 7.3
• Linux: gcc 5.3 or 6.1 (gcc 4.9 is not supported by json-struct module)

Processing

• Make database from the source fasta files.

    seqdb-create --db ~/WHO/seqdb.json.xz *.fasta
  

• Generate phylogenetic tree on albertine

    whocc-make-tree --flu-lineage BYAM --raxml-num-runs 128 --garli-num-runs 128
  

  Various output files will be under /syn/eu/ac/results/whocc-tree

• Export some sequences into fasta (or phylip)

    seqdb-export -h
  

• Importing tree from newick format

    tree-to-tree -h
  

• Drawing tree

    tree-draw -h
  

• TODO

  • http://www.libharu.org/ (2015-06-28) (homebrew) HPDF_Page_CreateTextAnnot

  • http://podofo.sourceforge.net (0.9.4 - 2016-06-08, 0.9.3 - 2014) (homebrew and apt-get)

  • http://www.jagpdf.org (Oct 2009)