Makefile.models

# -*- makefile-gmake -*-

# Common substitution models
presets: $(addprefix src/,$(addsuffix .h,jc jcrna lg dayhoff jones wag ECMrest ECMunrest))

# model/lg.json is the matrix from this paper, estimated from Pfam using XRATE:
#  An improved general amino acid replacement matrix.
#  Le SQ, Gascuel O.
#  Mol Biol Evol. 2008 Jul;25(7):1307-20. doi: 10.1093/molbev/msn067
#  https://www.ncbi.nlm.nih.gov/pubmed/18367465

# model/dayhoff.json:
#  Dayhoff MO, Schwartz RM, Orcutt BC. 1978.
#  A model of evolutionary change in proteins.
#  In: Atlas of Protein Sequence and Structure. M.O. Dayhoff, ed., pp. 345–352.

# model/jones.json:
#  Jones D.T., Taylor W.R. and Thornton J.M. 1992.
#  The rapid generation of mutation data matrices from protein sequences.
#  CABIOS 8:275-282

# model/wag.json:
#  Whelan, S. and N. Goldman.  2001.
#  A general empirical model of protein evolution derived from multiple protein families
#  using a maximum likelihood approach.
#  Molecular Biology and Evolution 18, 691-699.

# lg.dat downloaded from this URL on 10/22/2016:
#  http://www.atgc-montpellier.fr/download/datasets/models/lg_LG.PAML.txt

# dayhoff.dat, jones.dat and wag.dat were extracted from this CPAN archive on 10/22/2016:
#  http://cpansearch.perl.org/src/HVALVERDE/Mecom-1.13/paml4.7/dat/
# Several files in this archive are credited to Ziheng Yang, 1998.

model/%.json: model/amino/%.dat
	node/paml2json.js $< >$@

# model/ECMrest.json and model/ECMunrest.json are the empirical codon models from this paper:
#  An empirical codon model for protein sequence evolution.
#  Kosiol C, Holmes I, Goldman N.
#  Mol Biol Evol. 2007 Jul;24(7):1464-79.
#  https://www.ncbi.nlm.nih.gov/pubmed/17400572
# ECMrest is restricted (no multi-nucleotide mutations), ECMunrest is unrestricted.
# The tokenization scheme is as defined in perl/tokenize.pl and also in src/ctok.cpp
CODTOKENS := $(shell perl/tokenize.pl -alphabet)
model/ECM%.json: model/codon/ECM%.dat
	node/paml2json.js -a '$(CODTOKENS)' $< >$@

src/%.cpp src/%.h: model/%.json
	perl/model2cpp.pl $*

# Conversion of old-format xrate models to Historian JSON models
model/%.json: model/hsm/%.hsm
	perl/xrate2json.pl $< >$@

# The default amino acid model is Le & Gascuel (2008)
# The default codon model is the unrestricted model from Kosiol, Goldman & Holmes (2007)

# Example of adding discretized-gamma rate classes to a model
# (can now do this via -gamma and -shape parameters from within historian)
model/prot1-4.json: model/prot1.json
	perl/gamma-sites.pl $< -bins 4 -pretty -verbose >$@