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New port, biology/iqtree: Efficient phylogenomic software

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WWW: http://www.iqtree.org/
This commit is contained in:
Joseph Mingrone 2017-10-21 16:57:53 +00:00
parent ee28374909
commit 1027ca2f40
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=452595
4 changed files with 43 additions and 0 deletions
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1
biology/Makefile
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@ -37,6 +37,7 @@
SUBDIR += hmmer
SUBDIR += htslib
SUBDIR += iolib
SUBDIR += iqtree
SUBDIR += jalview
SUBDIR += jellyfish
SUBDIR += lagan

24
biology/iqtree/Makefile Normal file
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# $FreeBSD$
PORTNAME= iqtree
DISTVERSIONPREFIX= v
DISTVERSION= 1.6.beta4
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
COMMENT= Efficient phylogenomic software by maximum likelihood
LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/eigen3.pc:math/eigen3
RUN_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/eigen3.pc:math/eigen3
USES= cmake compiler:openmp
USE_GITHUB= yes
GH_ACCOUNT= Cibiv
PLIST_FILES= bin/iqtree example.cf example.nex example.phy models.nex
WRKSRC= ${WRKDIR}/IQ-TREE-${DISTVERSION}
.include <bsd.port.mk>

3
biology/iqtree/distinfo Normal file
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TIMESTAMP = 1508602968
SHA256 (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 78ff4cb03140aa36f5e057e0182f304e83f46cb729e09a1ef08ce9720bcce04f
SIZE (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 4450460

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biology/iqtree/pkg-descr Normal file
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IQ-TREE is efficient and versatile phylogenomic software, created as the
successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). Development was
motivated by the rapid accumulation of phylogenomic data, leading to a need for
efficient phylogenomic software that can handle a large amount of data and
provide more complex models of sequence evolution. To this end, IQ-TREE can
utilize multicore computers and distributed parallel computing to speed up the
analysis. IQ-TREE automatically performs checkpointing to resume an interrupted
analysis.
As input IQ-TREE accepts all common sequence alignment formats including PHYLIP,
FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable
report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be
visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.
WWW: http://www.iqtree.org/