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Mac OS X Software for Genetic Linkage Studies

Please note that by making these package installers available, we are not providing a guarentee that these programs work properly, nor are we endorsing any results generated with these programs. We have (in most cases) simply taken freely available source code and modified it to compile under OS X. Only minimal testing of the resulting binaries was done, so check back for updated versions from time to time (we'll fix problems if and when we find them and create new packages). Where appropriate, we have created individual installers and returned these to the original authors for distribution.
These packages install software in the /usr/local directories. Most binaries will be placed in /usr/local/bin, and most accessory scripts (shell and perl scripts) will be placed in /usr/local/scripts. If these directories do not exist, they will be created for you. It is up to the user to add these directories to their shell-specific default PATH environment variable.

Available Packages

  • Core Linkage Apps - (version 2; 4/20/05) - this package provides the following software:
    • genehunter (v2.1_r5b)
    • genehunter-plus (v1.2)
    • clump (v2.2)
    • unphased (cocaphase/tdtphase/pdtphase/qtphase/qpdtphase) (v2.401)
    • eh/ehplus/fehp/pm/pmplus (v1.1/v1.2)
    • fbat (v1.7.2)
    • hap (v0.2.1)
    • haploxt (v1.1)
    • phase (v2.0.2)
    • recode (v1.5)
    • simulate (v2.24)
    • loki (v2.5.4)
    • splink (v1.09)
    • superlink (v1.4)
    • tdtlikena (v2.1)
    • tdtpowercalc (v1.2.1)
    • transmit (v2.5.4)

  • Aspex - (version 2.5) - this package provides the following software:
    • sib_ibd
    • sib_kin
    • sib_map
    • sib_phase
    • sib_tdt
    • sib_clean
    • list_incompat
    • list_untyped
    • xmgr_map
    • rec_dist
    • ligate
    • restrict

  • Merlin - (version 1.0.1; Download directly from Dr. Abecasis' web site) - this package provides the following software:
    • merlin
    • merlin-regress
    • minx
    • pedstats (v0.6.4)
    • pedmerge
    • pedwipe

  • QTDT - (version 2.5.1; Download directly from Dr. Abecasis' web site) - this package provides the following software:
    • qtdt
    • prelude
    • finale
    • pedstats (v0.6.4)

  • FASTLINK - (LINKAGE) - (version 4.1P) - this package provides the following software:
    • mlink
    • ilink
    • lodscore
    • linkmap
    • makeped
    • unknown
    • lsp
    • lrp
    • lcp