kgori

(cal:0.1,ctr:0.1,(lel:0.1,(pst:0.1,((dha:0.1,pgu:0.1):0.1,(yli:0.1,((cgl:0.1,(sca:0.1,(sba:0.1,(sku:0.1,(smi:0.1,(sce:0.1,spa:0.1):0.1):0.1):0.1):0.1):0.1):0.1,((kwa:0.1,skl:0.1):0.1,(ago:0.1,kla:0.1):0.1):0.1):0.1):0.1):0.1):0.1):0.1);

kgori

diff --git a/src/Bpp/Exceptions.h b/src/Bpp/Exceptions.h
index 2ac2c53..ce62920 100644
--- a/src/Bpp/Exceptions.h
+++ b/src/Bpp/Exceptions.h
@@ -44,6 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.

 #include <stdexcept>
 #include <vector>
+#include <string>

kgori

diff --git a/src/mem_alloc.h b/src/mem_alloc.h
index 4dc4ce7..88828e0 100644
--- a/src/mem_alloc.h
+++ b/src/mem_alloc.h
@@ -2,7 +2,9 @@
 #define __mem_alloc_h
 #include <stddef.h>
 #include <stdlib.h>
+#ifdef __linux__
 #include <malloc.h>

kgori

import re

# Fasta one-liners
# Parse fasta from a string
def fasta_parse_string(s):
    return dict([(lambda x:(x[0].strip(), re.sub(r'\s+','',x[2])))(l.partition('\n')) for l in s.split('>')[1:]])

# Parse fasta from a file
def fasta_parse_file(f):
    with open(f) as h:return fasta_parse_string(h.read())

kgori

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {

kgori

// RAXML code for setting up likelihood tip vectors for different characters
				//TGCA - notes added KG
	meaningDNA['A'] =  1;	//0001
	meaningDNA['B'] = 14;	//1110
	meaningDNA['C'] =  2;	//0010
	meaningDNA['D'] = 13;	//1101
	meaningDNA['G'] =  4;	//0100
	meaningDNA['H'] = 11;	//1011
	meaningDNA['K'] = 12;	//1100
	meaningDNA['M'] =  3;	//0011

kgori

kgori

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {