PHAST\uff1aPhylogenetic Analysis with Space\/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.<\/p>\n
Major PHAST programs\uff1a<\/p>\n
phastCons<\/a>: Conservation scoring and identification of conserved elements \u5b89\u88c5PHAST\uff1a<\/p>\n PHAST\uff1aPhylogenetic Analysis with Space\/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/521"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=521"}],"version-history":[{"count":1,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/521\/revisions"}],"predecessor-version":[{"id":522,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/521\/revisions\/522"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=521"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=521"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=521"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\nphyloFit<\/a>: Fitting of phylogenetic models to aligned DNA sequences
\nphyloP<\/a>: Computation of p-values for conservation or acceleration, either lineage-specific or across all branches
\nphastOdds<\/a>: Log-odds scoring for phylogenetic models or phylo-HMMs
\nexoniphy<\/a>: Phylogenetic exon prediction
\ndless<\/a>: Prediction of elements under lineage-specific selection
\nprequel<\/a>: Probabilistic reconstruction of ancestral sequences
\nphastBias<\/a>: Identification of GC-biased gene conversion using a phylo-HMM<\/p>\nwget -c http:\/\/www.netlib.org\/clapack\/clapack.tgz\r\ntar -xvzf clapack.tgz\r\ncd CLAPACK-3.2.1\r\ncp make.inc.example make.inc && make f2clib && make blaslib && make lib\r\nwget -c http:\/\/compgen.cshl.edu\/phast\/downloads\/phast.v1_5.tgz\r\ntar zxf phast.v1_5.tgz\r\ncd phast\/src\/\r\nmake CLAPACKPATH=\/opt\/biosoft\/CLAPACK-3.2.1\r\necho 'PATH=$PATH:\/opt\/biosoft\/phast\/bin' >> ~\/.bashrc\r\nsource ~\/.bashrc<\/pre>\n","protected":false},"excerpt":{"rendered":"