Commit 8f5b8289 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.6.12+dfsg

parent 93437d2c

CMakeLists.txt

+3 −3
Original line number Diff line number Diff line
@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE) 
# The version number.

set (iqtree_VERSION_MAJOR 1)

set (iqtree_VERSION_MINOR 6)

set (iqtree_VERSION_PATCH "11")

set (iqtree_VERSION_PATCH "12")



set(BUILD_SHARED_LIBS OFF)
@@ -277,10 +277,10 @@ if (NOT IQTREE_FLAGS MATCHES "single") 
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")

  		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")

  	elseif (CLANG)

        if (APPLE)

        if (APPLE OR WIN32)

            set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")

            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -pthread")

            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Xpreprocessor -fopenmp -lomp")

            set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lomp")

        else()

            set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")

            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")

README.md

+2 −0
Original line number Diff line number Diff line 
IQ-TREE

=======



[![Github All Releases](https://img.shields.io/github/downloads/Cibiv/IQ-TREE/total.svg?style=social&logo=github&label=Download)](https://github.com/Cibiv/IQ-TREE/releases)

[![BioConda downloads](https://img.shields.io/conda/dn/bioconda/iqtree.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/iqtree)

[![Build Status](https://travis-ci.org/bqminh/IQ-TREE.svg?branch=master)](https://travis-ci.org/bqminh/IQ-TREE)

[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)

alignment/alignment.cpp

+1 −1
Original line number Diff line number Diff line
@@ -312,7 +312,7 @@ Alignment *Alignment::removeIdenticalSeq(string not_remove, bool keep_two, StrVe 
        if (checked[seq1]) continue;

        bool first_ident_seq = true;

		for (int seq2 = seq1+1; seq2 < getNSeq(); seq2++) {

			if (getSeqName(seq2) == not_remove) continue;

			if (getSeqName(seq2) == not_remove || removed[seq2]) continue;

			bool equal_seq = true;

			for (iterator it = begin(); it != end(); it++)

				if  ((*it)[seq1] != (*it)[seq2]) {

alignment/alignmentpairwise.cpp

+13 −4
Original line number Diff line number Diff line
@@ -259,17 +259,26 @@ void AlignmentPairwise::computeFuncDerv(double value, double &df, double &ddf) { 


    for (cat = 0; cat < ncat; cat++) {

        double rate_val = site_rate->getRate(cat);

        double prop_val = site_rate->getProp(cat);

        if (tree->getModelFactory()->site_rate->getGammaShape() == 0.0)

            rate_val = 1.0;



        double rate_sqr = rate_val * rate_val;

        double coeff1 = rate_val * prop_val;

        double coeff2 = rate_val * coeff1;

        tree->getModelFactory()->computeTransDerv(value * rate_val, trans_mat, trans_derv1, trans_derv2);

        for (i = 0; i < trans_size; i++) {

            sum_trans[i] += trans_mat[i];

            sum_derv1[i] += trans_derv1[i] * rate_val;

            sum_derv2[i] += trans_derv2[i] * rate_sqr;

            sum_trans[i] += trans_mat[i] * prop_val;

            sum_derv1[i] += trans_derv1[i] * coeff1;

            sum_derv2[i] += trans_derv2[i] * coeff2;

        }

    }

    

    // 2019-07-03: incorporate p_invar

    double p_invar = site_rate->getPInvar();

    if (p_invar > 0.0)

        for (i = 0; i < num_states; i++)

            sum_trans[i*num_states+i] += p_invar;

    

    for (i = 0; i < trans_size; i++)

        if (pair_freq[i] > Params::getInstance().min_branch_length && sum_trans[i] > 0.0) {

//            lh -= pair_freq[i] * log(sum_trans[i]);

alignment/superalignment.cpp

+1 −1
Original line number Diff line number Diff line
@@ -664,7 +664,7 @@ Alignment *SuperAlignment::removeIdenticalSeq(string not_remove, bool keep_two, 
        if (checked[seq1]) continue;

        bool first_ident_seq = true;

		for (int seq2 = seq1+1; seq2 < getNSeq(); seq2++) {

			if (getSeqName(seq2) == not_remove) continue;

			if (getSeqName(seq2) == not_remove || removed[seq2]) continue;

			bool equal_seq = true;

			int part = 0;

			// check if seq1 and seq2 are identical over all partitions