Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 452594) +++ head/biology/Makefile (revision 452595) @@ -1,115 +1,116 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib + SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/iqtree/Makefile =================================================================== --- head/biology/iqtree/Makefile (nonexistent) +++ head/biology/iqtree/Makefile (revision 452595) @@ -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 Property changes on: head/biology/iqtree/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/iqtree/distinfo =================================================================== --- head/biology/iqtree/distinfo (nonexistent) +++ head/biology/iqtree/distinfo (revision 452595) @@ -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 Property changes on: head/biology/iqtree/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/iqtree/pkg-descr =================================================================== --- head/biology/iqtree/pkg-descr (nonexistent) +++ head/biology/iqtree/pkg-descr (revision 452595) @@ -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/ Property changes on: head/biology/iqtree/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property