Skip to content

Commit

Permalink
Nick's README for 7.0
Browse files Browse the repository at this point in the history
  • Loading branch information
MatthewMah committed Jun 24, 2020
1 parent 24e63b5 commit 0cb8e45
Showing 1 changed file with 26 additions and 2 deletions.
28 changes: 26 additions & 2 deletions README
Original file line number Diff line number Diff line change
@@ -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.

Expand Down Expand Up @@ -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 <[email protected]>

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
Expand All @@ -57,11 +60,32 @@ beyond our scope.
Nick Patterson
<[email protected]>


*** 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
<executable> or <executable> -h to get brief documentation or

*** NEW ***
*** Fairly NEW ***
Alter number of chromosomes:
numchrom: <zzz>
zzz should be the autosome number (default 22 -- the number for humans)
Expand Down

0 comments on commit 0cb8e45

Please sign in to comment.