kgori

# -*- 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

#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

kgori

kgori

kgori

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

kgori

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

kgori

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "discrete_gamma.h"
// PAML code for discrete gamma

// Forward decs
double QuantileChi2(double prob, double v);
double LnGammaFunction(double alpha);
double IncompleteGamma(double x, double alpha, double ln_gamma_alpha);

kgori

import numpy as np

def setup_logger():
    import logging
    logger = logging.getLogger()
    for handler in logger.handlers:
        logger.removeHandler(handler)
    ch=logging.StreamHandler()
    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
    ch.setFormatter(formatter)