HMMer

HMMer → Hidden Markov Model package from Sean Eddy

HMMer은 hidden markov models을 적용한 수학적인 방법을 기초로하여 개발된것으로, 
모든 염기 서열을 인지한 후 multiple alignment를 통해 비교 가능한 염기 서열을 찾아낸다. 


관련문서 : http://hmmer.wustl.edu/#overview
=============================================================================
Download : http://hmmer.wustl.edu/#download

Source code version

Download: hmmer-2.3.2.tar.gz

AMD Opteron/Linux

Download: hmmer-2.3.2.bin.amd-opteron-64-suse-linux.tar.gz
Opteron 242, 2x1.6 GHz; SUSE Linux; GCC 3.3.3; --enable-threads --enable-lfs
[Contributed by Martin Gollery, University of Nevada, Reno.]
RPMs built with the Portland Group C compiler are also available from Joe Landman and Scalable Informatics, LLC:
you can download hmmer-2.3.2-5pgi.x86_64_pgi.rpm from their site.

Apple Macintosh PowerPC OS/X

Download: hmmer-2.3.2.bin.powerpc-apple-osx.tar.gz
Apple PowerPC; 2x G4/1.25Ghz; OS/X Darwin 6.8; --enable-threads --enable-lfs --enable-altivec; CFLAGS="-O"
Includes Altivec optimizations contributed by Erik Lindahl, Stanford University.

Compaq Alpha Tru64

Download: hmmer-2.3.2.bin.alpha-tru64.tar.gz
Compaq Alpha ES40; Tru64 5.1B; --enable-threads --enable-lfs; CC=cc CFLAGS=-O

Compaq Alpha Linux

Download: hmmer-2.3.2.bin.alpha-linux.tar.gz
Compaq Alpha ES40; Red Hat Alpha Linux 7.1; --enable-threads --enable-lfs; CFLAGS=-O

Hewlett/Packard IA64 (Itanium2), Linux

Download: hmmer-2.3.2.bin.ia64-hp-linux.tar.gz
HP rx2600; 2xItanium2/900/1.5; Linux 2.4.18-e.12; --enable-threads --enable-lfs; CFLAGS="-O2"

Hewlett/Packard IA64 (Itanium2), HP/UX

Download: hmmer-2.3.2.bin.ia64-hp-hpux.tar.gz
HP rx2600; 2xItanium2/900/1.5; HP/UX 11.22; --enable-threads --enable-lfs; CC=cc CFLAGS="-O"

 

IBM Power4, Linux

Download: hmmer-2.3.2.bin.ibm-pwr4-suse-linux.tar.gz
IBM pSeries; Power4; SusE Linux 8 (SLES8); --enable-threads --enable-lfs; CC=xlc_r CFLAGS="-O -q64 -qtune=pwr4 -qcache=auto"
[Provided by Bob Arenburg and IBM Life Sciences.]

 

IBM Power4, AIX

Download: hmmer-2.3.2.bin.ibm-aix.tar.gz
IBM pSeries 630; 4xPower4/1.2GHz; AIX 5.2; --enable-threads --enable-lfs; CC=xlc_r CFLAGS="-O2"
On large multiprocessor systems (8 cpus or more), you want to add "-bmaxdata:0x80000000" to CFLAGS and recompile to enable AIX's "Large Program Support"; otherwise, AIX only allows a program to allocate 256 MB of RAM by default.

Intel FreeBSD

Download: hmmer-2.3.2.bin.intel-freebsd.tar.gz
Dell 1550/VMWare; 2xPIII/1.27/512K; FreeBSD 4.7; --enable-threads --enable-lfs; CFLAGS="-O2 -static"

Intel GNU/Linux

Download: hmmer-2.3.2.bin.intel-linux.tar.gz
Or, as an RPM: hmmer-2.3.2-1static_pvm.i686.rpm
Dell 6450; 4xPIII/700/2; Red Hat Linux 7.2; --enable-threads --enable-lfs --enable-pvm; CC=icc CFLAGS="-O3 -axMKW -static"
the RPM spec file is available: hmmer-pvm.spec

Intel OpenBSD

Download: hmmer-2.3.2.bin.intel-openbsd.tar.gz
Dell 1550/VMWare; 2xPIII/1.27/512K; OpenBSD 3.2; --enable-threads --enable-lfs; CFLAGS="-O2 -static"

Intel Solaris

Download: hmmer-2.3.2.bin.intel-solaris.tar.gz
Dell 1550/VMWare; 2xPIII/1.27/512K; x86 Solaris 9; --enable-threads --enable-lfs; CFLAGS="-O2"

Silicon Graphics IA64 (Itanium2), Linux

Download: hmmer-2.3.2.bin.ia64-sgi-linux.tar.gz
Silicon Graphics Altix 3000; 16xItanium2/900/1.5; Linux 2.4.19; --enable-threads --enable-lfs; CFLAGS="-O2 -static"

Silicon Graphics MIPS IRIX

Download: hmmer-2.3.2.bin.sgi-irix64.tar.gz
Silicon Graphics Origin200; 4xMIPS R10K/180,195/2; IRIX 6.5.12; --enable-threads --enable-lfs; CFLAGS="-O2 -static"

Sun Sparc Solaris

[The Solaris box in our compile farm has recently decided to quit, after years of faithful service. For now, build from the source release instead. We have one report that 2.3.2 does not compile cleanly on Solaris 8: you may need to manually add -lnsl to LIBS in src/Makefile, after running ./configure. We will resolve this in a subsequent release, as soon as we have access to Solaris again.] 
=============================================================================