#Phast license archive
#Phast license software
#Phast license series
#Phast license download

In addition, it supports some phylogenetic modeling features not available in other packages, such as context-dependent subsitution models and model fitting by expectationРІР‚вЂњmaximization. However, PHAST is unique in that it combines phylogenetic modeling and functional element identification. PHAST has some overlap with the popular phylogenetic modeling package PAML as well as with other packages for phylogenetics such as HYPHY and MEGA, tools for conservation analysis such as GERP and SCONE, and comparative gene finders such as N-SCAN. As of September 2010, the package has been downloaded more than 1000 times (counting unique IP addresses). PHAST is best known as the engine behind several popular tracks in the UCSC Genome Browser (including, most notably, the Conservation track), but it can also be downloaded and installed for use in custom analyses not available through the browser. Over time, however, as the package has expanded in functionality, it has gradually been adopted by a fairly large group of researchers from the broader comparative genomics community. (The phrase РІР‚Вspace/time modelsРІР‚в„ў, borrowed from Yang, reflects the prominent role of phylogenetic hidden Markov models in the package.) Our initial goal in developing PHAST was to support our own research in comparative genomics.

#Phast license software

Since 2002, we have been developing a software package, called PHylogenetic Analysis with Space/Time models (PHAST), that consists of a collection of programs and supporting libraries for statistical phylogenetic modeling and functional element identification. Methods of this kind have been used to identify evolutionary conserved elements, novel protein-coding genes, fast-evolving noncoding sequences, transcription factor binding sites, noncoding RNAs and other types of functional elements. Of particular interest are statistical, phylogenetic methods for characterizing rates and patterns of molecular evolution and for identifying sequences under natural selection against a background of neutral evolution.

#Phast license archive

RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN ).Р”Р„s complete genome sequences have become available for large numbers of closely related organisms, interest has steadily grown in improved computational methods for comparative genomics.

#Phast license download

PHAST v1.0 and RPHAST v1.0 are available for download at, under the terms of an unrestrictive BSD-style license. The R interface also makes the PHAST libraries acccessible to non-C programmers, and is useful for rapid prototyping. We demonstrate that RPHAST can be particularly useful in applications involving both large-scale phylogenomics and complex statistical analyses.

#Phast license series

In addition, we introduce a new interface to the PHAST libraries from the R statistical computing environment, called RPHAST, and illustrate its use in a series of vignettes. We outline the components of the package and detail recent improvements. Here, we describe the first official release (v1.0) of PHAST, with improved stability, portability and documentation and several new features. PHAST has been in development since 2002 and has now been downloaded more than 1000 times, but so far it has been released only as provisional (РІР‚ВbetaРІР‚в„ў) software. However, it also includes several other tools for phylogenetic modeling and functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations. PHAST is best known as the engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser. The PHylogenetic Analysis with Space/Time models (PHAST) software package consists of a collection of command-line programs and supporting libraries for comparative genomics.