Date: Tue, 26 Feb 2019 15:12:43 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493971 - head/biology/paml Message-ID: <201902261512.x1QFChvk082223@repo.freebsd.org>
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Author: jrm Date: Tue Feb 26 15:12:42 2019 New Revision: 493971 URL: https://svnweb.freebsd.org/changeset/ports/493971 Log: biology/paml: Update to version 4.9i 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. Modified: head/biology/paml/Makefile (contents, props changed) head/biology/paml/distinfo (contents, props changed) head/biology/paml/pkg-plist (contents, props changed) Modified: head/biology/paml/Makefile ============================================================================== --- head/biology/paml/Makefile Tue Feb 26 14:58:27 2019 (r493970) +++ head/biology/paml/Makefile Tue Feb 26 15:12:42 2019 (r493971) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= paml -PORTVERSION= 4.9h +PORTVERSION= 4.9i CATEGORIES= biology MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/ DISTNAME= ${PORTNAME}${DISTVERSION} @@ -13,6 +13,7 @@ COMMENT= Phylogenetic Analysis by Maximum Likelihood ( LICENSE= GPLv3 USES= dos2unix gmake tar:tgz + DOS2UNIX_GLOB= *.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \ *.trees *.txt *.xml paupblock paupend Modified: head/biology/paml/distinfo ============================================================================== --- head/biology/paml/distinfo Tue Feb 26 14:58:27 2019 (r493970) +++ head/biology/paml/distinfo Tue Feb 26 15:12:42 2019 (r493971) @@ -1,3 +1,3 @@ -TIMESTAMP = 1524675240 -SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3 -SIZE (paml4.9h.tgz) = 6241149 +TIMESTAMP = 1551192920 +SHA256 (paml4.9i.tgz) = bc11af500b88d977a8765161f6c014f178273cbd887657eebd6330a3a967b4cc +SIZE (paml4.9i.tgz) = 6556407 Modified: head/biology/paml/pkg-plist ============================================================================== --- head/biology/paml/pkg-plist Tue Feb 26 14:58:27 2019 (r493970) +++ head/biology/paml/pkg-plist Tue Feb 26 15:12:42 2019 (r493971) @@ -77,6 +77,7 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/FigTree.tre %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
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