From owner-svn-ports-head@freebsd.org Tue Feb 26 15:12:44 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 5BC21151C73F; Tue, 26 Feb 2019 15:12:44 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id EAAAE89C67; Tue, 26 Feb 2019 15:12:43 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 9F3606EB9; Tue, 26 Feb 2019 15:12:43 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x1QFChVC082228; Tue, 26 Feb 2019 15:12:43 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x1QFChvk082223; Tue, 26 Feb 2019 15:12:43 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <201902261512.x1QFChvk082223@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Tue, 26 Feb 2019 15:12:43 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493971 - head/biology/paml X-SVN-Group: ports-head X-SVN-Commit-Author: jrm X-SVN-Commit-Paths: head/biology/paml X-SVN-Commit-Revision: 493971 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: EAAAE89C67 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.998,0]; NEURAL_HAM_SHORT(-0.96)[-0.964,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 26 Feb 2019 15:12:44 -0000 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