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Kevin Gori kgori

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kgori / biopython--concatenate.ipynb
Created June 17, 2015 11:51
Concatenate alignments with biopython
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kgori / Concatenate alignments.ipynb
Last active August 29, 2015 14:22
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kgori / search_algo_patch
Last active August 29, 2015 14:21
Patch searchAlgo.c
diff --git a/src/searchAlgo.c b/src/searchAlgo.c
index c0547b0..3c1a578 100644
--- a/src/searchAlgo.c
+++ b/src/searchAlgo.c
@@ -2711,7 +2711,7 @@ pllComputeTBR (pllInstance * tr, partitionList * pr, nodeptr p, int mintrav,
@return
The likelihood yielded from the NNI
*/
-static double
+double
@kgori
kgori / pll_h_patch
Last active August 29, 2015 14:21
pll.h patch
diff --git a/src/pll.h b/src/pll.h
index 6941efb..572179c 100644
--- a/src/pll.h
+++ b/src/pll.h
@@ -123,7 +123,7 @@ extern "C" {
#define PLL_BADREAR -1
-#define PLL_NUM_BRANCHES 50
+#define PLL_NUM_BRANCHES 5000
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kgori / parse_orthoxml.ipynb
Created March 10, 2015 14:07
Parse OrthoXML
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kgori / gene_tree_tracer_example.ipynb
Created March 10, 2015 13:37
gene_tree_tracer_example
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kgori / pll.c
Created November 11, 2014 15:37
Basic tree builder using PLL, outputs all parameters
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <pll/pll.h>
#define EXIT_NO_OVERWRITE 4
#define EXIT_INCOMPATIBLE_TREE_ALIGNMENT 3
#define EXIT_PARTITIONS_PARSE_FAILURE 2
#define EXIT_ALIGNMENT_PARSE_FAILURE 1
#define EXIT_SUCCESS 0
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kgori / gist:4329149770a5d0dd6092
Created November 11, 2014 15:22
# -*- coding: utf-8 -*-
from __future__ import print_function
try:
from setuptools import setup, find_packages, Extension
except ImportError:
from distutils.core import setup, Extension
def find_packages():
return ['treeCl']
try:
from Cython.Distutils import build_ext
@kgori
kgori / pll_patch
Created October 7, 2014 17:34
pll patch
--- a/configure.ac
+++ b/configure.ac
@@ -4,7 +4,7 @@
AC_PREREQ([2.68])
AC_INIT([libpll], [1.0.0], [Tomas.Flouri@h-its.org])
AC_CONFIG_MACRO_DIR([m4])
-AM_INIT_AUTOMAKE
+AM_INIT_AUTOMAKE([subdir-objects])
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kgori / LG08_model.py
Created October 1, 2014 15:38
PyCogent model specification for Le and Gascuel LG08 model
import numpy
from cogent.evolve import substitution_model
LG08_freqs = {
'A': 0.079066, 'C': 0.012937,
'D': 0.053052, 'E': 0.071586,
'F': 0.042302, 'G': 0.057337,
'H': 0.022355, 'I': 0.062157,