mirror of
https://git.FreeBSD.org/ports.git
synced 2025-01-13 07:34:50 +00:00
4fb4ec21f6
Upstream changes as described by the author: - mcmctree: I have added an option (duplication = 1) for dating a tree with both speciations and gene duplications, so that some nodes on the tree share divergence times. Nodes sharing ages are identified using labels in the tree file: #1, #2, .... I have yet to update the document about specification of the model. - mcmctree: The TipDate option was written for one locus or partition and never worked for more than two loci/partitions. I have edited the code so that it works for multiple partitions, some of which may be molecular and the others morphological. - codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7 (FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This option uses the observed codon or amino acid frequencies for the mutation-selection models of codon usage. Instead the program estimates the frequencies using maximum likeihood, which is what the option estFreq = 1 does. Look at the README file in the examples/mtCDNAape/ folder. - codeml clade model D: The bounds for the w (dN/dS) ratios in the first site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model D in 4.9b. The motivation for the bounds is that site class 0 represents strong purifying selection with a small w0, while site class 1 should include sites under weak purifying selection with a larger w1. However the bounds are arbitrary. In some datasets, the MLEs are found to be at the bounds, making the interpretation awkward. I have changed the bounds to the following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user should swap the estimates of w0 and w2 if w0 > w1.
55 lines
1.5 KiB
Makefile
55 lines
1.5 KiB
Makefile
# Created by: dbader@eece.unm.edu
|
|
# $FreeBSD$
|
|
|
|
PORTNAME= paml
|
|
PORTVERSION= 4.9i
|
|
CATEGORIES= biology
|
|
MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
|
|
DISTNAME= ${PORTNAME}${DISTVERSION}
|
|
|
|
MAINTAINER= jrm@FreeBSD.org
|
|
COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
|
|
|
|
LICENSE= GPLv3
|
|
|
|
USES= dos2unix gmake tar:tgz
|
|
|
|
DOS2UNIX_GLOB= *.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
|
|
*.trees *.txt *.xml paupblock paupend
|
|
|
|
BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \
|
|
evolverNSbranchsites evolverNSsites pamp yn00
|
|
|
|
OPTIONS_DEFINE= DOCS EXAMPLES
|
|
|
|
post-extract:
|
|
@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
|
|
|
|
do-build:
|
|
@cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
|
|
.for f in NSbranches NSsites NSbranchsites
|
|
@cd ${WRKSRC}/src && \
|
|
${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
|
|
.endfor
|
|
|
|
do-install:
|
|
.for f in ${BINARIES}
|
|
${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
|
|
.endfor
|
|
|
|
do-install-DOCS-on:
|
|
@${MKDIR} ${STAGEDIR}${DOCSDIR}
|
|
${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
|
|
${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
|
|
|
|
do-install-EXAMPLES-on:
|
|
@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
|
|
(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
|
|
${STAGEDIR}${EXAMPLESDIR})
|
|
(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
|
|
.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
|
|
${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
|
|
.endfor
|
|
|
|
.include <bsd.port.mk>
|