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| author | jrm <jrm@FreeBSD.org> | 2017-10-22 00:57:53 +0800 |
|---|---|---|
| committer | jrm <jrm@FreeBSD.org> | 2017-10-22 00:57:53 +0800 |
| commit | e856196c0a31654bc9ca9ad2956c76f06cd82b9e (patch) | |
| tree | d22999ff47193befd945f620f0ea74374fb18921 /biology | |
| parent | 9a614b163f0ab5de20bc9e1ff7c535fca8fbefeb (diff) | |
| download | freebsd-ports-gnome-e856196c0a31654bc9ca9ad2956c76f06cd82b9e.tar.gz freebsd-ports-gnome-e856196c0a31654bc9ca9ad2956c76f06cd82b9e.tar.zst freebsd-ports-gnome-e856196c0a31654bc9ca9ad2956c76f06cd82b9e.zip | |
New port, biology/iqtree: Efficient phylogenomic software
WWW: http://www.iqtree.org/
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/iqtree/Makefile | 24 | ||||
| -rw-r--r-- | biology/iqtree/distinfo | 3 | ||||
| -rw-r--r-- | biology/iqtree/pkg-descr | 15 |
4 files changed, 43 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 98c0bb8296fd..ce25330879fb 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -37,6 +37,7 @@ SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib + SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += lagan diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile new file mode 100644 index 000000000000..55a984e11ffe --- /dev/null +++ b/biology/iqtree/Makefile @@ -0,0 +1,24 @@ +# $FreeBSD$ + +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> diff --git a/biology/iqtree/distinfo b/biology/iqtree/distinfo new file mode 100644 index 000000000000..45ad53376bf8 --- /dev/null +++ b/biology/iqtree/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1508602968 +SHA256 (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 78ff4cb03140aa36f5e057e0182f304e83f46cb729e09a1ef08ce9720bcce04f +SIZE (Cibiv-iqtree-v1.6.beta4_GH0.tar.gz) = 4450460 diff --git a/biology/iqtree/pkg-descr b/biology/iqtree/pkg-descr new file mode 100644 index 000000000000..5e10f7dbdebe --- /dev/null +++ b/biology/iqtree/pkg-descr @@ -0,0 +1,15 @@ +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/ |