From 0cb8e45b2da7e01a288792e1f42079b95c19f9e2 Mon Sep 17 00:00:00 2001 From: Matthew Mah Date: Wed, 24 Jun 2020 11:49:49 -0400 Subject: [PATCH] Nick's README for 7.0 --- README | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/README b/README index c0a3030..9a83bda 100644 --- a/README +++ b/README @@ -1,4 +1,4 @@ -ADMIXTOOLS version 7.0 6/23/20 (for Linux and Mac) +ADMIXTOOLS version 7.0 6/24/20 (for Linux and Mac) See README.INSTALL for installation info. @@ -42,6 +42,9 @@ If you have issues with missing lapacke symbols, for example "undefined referenc Similarly for Ubuntu, for "undefined reference to dspev_" 'make LDLIBS="-llapack"' +For questions about building this software: +Matthew Mah + If you have trouble compiling and running our code, try compiling and running the examples in the examples/ directory. Download the example datasets from https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz @@ -57,11 +60,32 @@ beyond our scope. Nick Patterson + *** NEW *** +1) +Users of ADMIXTOOLS should know that an alternate version in R (native mode -- reimplementation) +written by Robert Maier is also available on Github. +See https://github.com/uqrmaie1/admixtools +Executables run fast, and it has features not available in this C version, such as interactive + exploration of graph phylogenies + +2) +version 7.0 has numerous upgrades. +a) Two new executables --qpfstats qpfmv allow precomputation of f-statistic basis. +This can greatly reduce computation costs. +b) qpAdm, qpWave, qpGraph support qpfstats output as input. +*** This is a much improved way of running with allsnps: YES. *** +c) A new experimental feature of qpGraph (halfscore: YES) allows + comparison of 2 phylogenies + a (weak) goodness of fit score. Be careful + if running with a large nnumber of populations and consider reducing block size say + blgsize: .005 + + +*** Fairly NEW *** Lightweight onlline documentation added, thanks to Eric Deveaud or -h to get brief documentation or -*** NEW *** +*** Fairly NEW *** Alter number of chromosomes: numchrom: zzz should be the autosome number (default 22 -- the number for humans)