BLAT: BLAST-Like Alignment Tool

BLAT is a legacy tool for sequence alignment that is not under active development.

New users should consider using razers3.

This is a fork of the BLAT package (v35) written by Jim Kent. The package has been restructured to ease compilation and installation. See the LICENSE.txt for conditions of use.

Remarks

No changes have been made to any of the header or source files. Therefore, all bugs (e.g. nondeterministic behaviour and memory leaks) are inherited from upstream.

For a BLAT package further stripped down to the minimal set of files and no external dependencies, see blat-lite.

For a minimal implementation of BLAT with the smallest code footprint, see mlat.

Installation

Prerequisite: libpng library and developmental headers.

If you are on Linux, no setup is necessary, and you can simply

make

Other details

If you’re on an alpha system, do the following before make:

setenv SOCKETLIB -lxnet

on Solaris, do

setenv SOCKETLIB "-lsocket -lnsl"

on SunOS, do

setenv SOCKETLIB "-lsocket -lnsl -lresolv"

The executables will be installed to bin within the package directory by default, the header files to include, and the libraries to lib. You may change ${DESTDIR} to change the prefix of the install path by:

DESTDIR=/usr/local make

Building static executables

See static-build.md.