commit jml

Author: simjoly

.gitignore

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+
+bin/jml_osx64
+
+bin/jml.exe
+
+*.xcworkspacedata
+
+*.xcuserstate
+
+*.xcbkptlist

JMLdoc.pdf

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+species =       bla nit fol pal pis gym set mul
+seqperspecies = 44     8      6         12        8         10         2        2
+locusrate = 0.8762
+heredityscalar = 1
+seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
+significancelevel = 0.1
+burnin = 0
+thinning = 1
+seed = -1

example_files/files with windows eol/jml.tpi.ctl

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+species =       bla nit fol pal pis gym set mul
+seqperspecies = 44     8      6         12        8         10         2        2
+locusrate = 0.8762
+heredityscalar = 1
+seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
+significancelevel = 0.1
+burnin = 0
+thinning = 1
+seed = -1

example_files/files with windows eol/rosa.species.trees

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+#readme file
+
+To analyse the example file, place the jml executable in this folder.
+
+On UNIX based systems, execute the following command:
+
+$ ./jml -c jml.tpi.ctl -t rosa.species.trees -d tpi.phy
+
+On windows systems, type:
+
+$ jml -c jml.tpi.ctl -t rosa.species.trees -d tpi.phy
+
+The program should perform 1000 simulations and then output the files "Distributions.txt", "Results.txt", and "Probabilities.txt".

example_files/files with windows eol/tpi.phy

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+/**********************************************************
+
+                       GenFunctions
+
+**********************************************************/
+
+
+/*
+
+    (c) Copyright 2002 by Michael J. Sanderson.
+
+    Permission is granted to copy and use this program provided 
+    no fee is charged for it and provided that this copyright 
+    notice is not removed.
+  
+
+    This file is part of Pofad, (c) Copyright 2005 by Simon Joly.
+
+    Pofad is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Pofad is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Foobar; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+
+
+#include <iostream>
+#include <stdio.h>
+#include <string>
+#include <stdlib.h>
+#include <ctype.h>
+
+#define MAX_TOKEN_SIZE 10000		/* we've got room */
+
+using namespace std;
+
+void			doGenericAlert(char* errorMsg);
+void			strtoupper(char *s);
+void 			fatal(char *s);