File	Date	Author	Commit
COPYING	2014-11-03	Alexander Klassmann	[b896de] license
INSTALL	2020-07-06	oneoverx	[5c1e6a] added instructions
M2fs.cpp	2014-11-11	oneoverx	[b71a31] removed dependency on boost
Makefile	2020-08-13	oneoverx	[783d72] parser API changed to constant parameters
Node.h	2015-03-02	oneoverx	[c94c67] added mutations
Nt3mom.m	2017-08-15	oneoverx	[64b95c] minor changes
README.txt	2020-07-06	oneoverx	[5a697d] corrected identation
Smom.cpp	2016-03-07	oneoverx	[a32ad5] added option -3
colmean.cpp	2016-02-11	oneoverx	[332588] renamed variable
condfsOutput.cpp	2016-03-01	oneoverx	[a3b59b] minor bug fix
fold.cpp	2018-04-02	oneoverx	[be3c99] extended to nested/disjoint spectra
fs3mom.cpp	2017-08-13	oneoverx	[1ab0c9] made skewness estimator unbiased
libsequenceMsScan.cpp	2020-08-13	oneoverx	[5fc4c8] alternative ms parser
m2IO.cpp	2016-02-26	oneoverx	[15343f] read from cin
m2diff.cpp	2016-02-26	oneoverx	[b06a2e] read from cin
m2elsum.cpp	2016-02-26	oneoverx	[539811] computes sum of array elements
m3IO.cpp	2016-02-26	oneoverx	[8c98ed] read from cin
m3diff.cpp	2016-02-26	oneoverx	[38e382] read from cin
m3elsum.cpp	2016-02-26	oneoverx	[598ab3] computes sum of array elements
matmean.cpp	2016-02-11	oneoverx	[13d25b] mean of matrices
ms2SF.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
ms2fastphase.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
ms2loci.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
ms2tikzhaplo.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
ms2tikztree.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
ms2vcf.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
msM2fs.cpp	2020-08-13	oneoverx	[fce688] parser API changed to constant parameters
msScan.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
msTsub.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
mscond.cpp	2020-08-13	oneoverx	[fce688] parser API changed to constant parameters
mscondfs.cpp	2020-08-13	oneoverx	[0f0a84] parser API changed to constant parameters
mscondfsCalc.cpp	2016-02-15	oneoverx	[b4d462] renamed
mscut.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
msfs.cpp	2020-08-13	oneoverx	[fce688] parser API changed to constant parameters
mssub.cpp	2020-08-13	oneoverx	[a49280] parser API changed to constant parameters
newicksubtree.cpp	2013-11-05	oneoverx	[9a8b86] modified comment, corrected main
nt2mom.cpp	2018-02-27	oneoverx	[ffaa86] exit after usage text
nt3mom.cpp	2016-12-07	oneoverx	[1d171c] changed command line arguments
ntdef.h	2018-02-25	oneoverx	[2aeecf] added finer distinctions of mutations
parseNewick.cpp	2015-08-28	oneoverx	[e84e88] minor change
testbias.cpp	2016-12-07	oneoverx	[abb6b2] renamed variable
tikzdef.h	2016-03-31	oneoverx	[689ed9] definitions for tikz
tree2tikz.cpp	2016-03-31	oneoverx	[f480c9] modified options and usage message
xi3mom.cpp	2016-12-09	oneoverx	[89825e] removed memory leak
xit1.cpp	2016-01-27	oneoverx	[90659e] changed preamble
xit2.cpp	2016-12-08	oneoverx	[08ae5d] changed init of harmonic numbers
xit3.cpp	2017-11-01	oneoverx	[bb0492] variabla naming conform to script
xit3_slow.cpp	2017-08-16	oneoverx	[48b259] updated function names

Read Me

License:
    The program package is released under the GNU General Public 
    License version 3.0 (GPLv3).

Credits:
    Alexander Klassmann
    
Compiling:
    To compile coatli, you should type 'make' in the coatli folder.  

Documentation:
    The latest version of the documentation and examples of usage can be 
    found at http://sourceforge.net/p/coatli/wiki/Home/

Getting Help:
    The best way to get help regarding coatli is to email the mailing
    list: coatli-help@lists.sourceforge.net 
    
Citation:
    If you make use of moment calculations provided by coatli in your research, I would appreciate a 
    citation of one of the two following papers:

    Ferretti, L., Klassmann, A., Raineri, E., Wiehe, T., Ramos-Onsins, S. E., & Achaz, G. (2018). 
    The expected neutral frequency spectrum of linked sites. Theoretical Population Biology, 1–10. 
    https://doi.org/10.1016/j.tpb.2018.06.001

    Klassmann, A., & Ferretti, L. (2018). 
    The third moments of the site frequency spectrum. Theoretical Population Biology, 120, 16–28. 
    https://doi.org/10.1016/j.tpb.2017.12.002