New upstream version 4.7

CONFIG ?= fltk-config

PDF_PS_FLAGS ?= -DNO_PDF

EXTRALIBS = `$(CONFIG) --use-images --ldflags`

EXTRALIBS = `$(CONFIG) --use-images --ldflags` -ldl -lpthread -lz

CC = gcc

CXX = g++

comlines.o resource.o nexus.o \

viewasprots.o racnuc_fetch.o concatenate.o statistics.o \

trees.o treedraw.o addbootstrap.o least_squares_brl.o \

pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o

pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o Fl_Native_File_Chooser_FLTK.o

COBJECTS = raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o

           HOW TO COMPILE SEAVIEW ON UNIX/LINUX SYSTEMS

The seaview program requires the FLTK library for its graphical user interface.

Version 1.3.0 or later of FLTK is necessary.

The FLTK library is available as packages for a number of Linux distributions.

If this package is installed on your system, go to step II.

If no such package is available for your system, or if version 1.3.0 is not available,

or if you don't want to use such package, you can compile the FLTK library as follows.

I COMPILING THE FLTK LIBRARY FROM SOURCE

========================================

The source code of the FLTK library is available at the "Download" item of http://www.fltk.org/.

- Get the stable release source archive, currently fltk-1.3.2-source.tar.gz

- Compile the FLTK library on your system:

   cd fltk-1.3.2

   ./configure

   make

It's not necessary to do "make install".

II COMPILING THE SEAVIEW PROGRAM

================================

First unpack the seaview source archive (seaview.tar.gz).

IIa Preparing the seaview makefile

If the FLTK library is installed on your system (i.e., include files in /usr/include/FL,

and libraries at /usr/lib/libfltk*), go to step IIb.

Otherwise, edit Makefile from the seaview source directory which contains these 5 lines:

FLTK = /usr/include

#uncomment the next 3 lines to use custom installed FLTK library

#FLTK = $(HOME)/fltk-1.3.2

#IFLTK = -I$(FLTK)

#LFLTK = -L$(FLTK)/lib

Transform these lines into:

#FLTK = /usr/include

#uncomment the next 3 lines to use custom installed FLTK library

FLTK = $(HOME)/fltk-1.3.2

IFLTK = -I$(FLTK)

LFLTK = -L$(FLTK)/lib

and also change the FLTK = $(HOME)/fltk-1.3.2 line so it gives the location in your system

of the top of the FLTK source tree.

IIb Compile/link the seaview program

In the seaview source directory, run

make

III Install seaview external programs

=====================================

Seaview drives 4 external programs (clustalo, muscle, Gblocks, phyml). Linux executables

of these are available from the linux items of http://pbil.univ-lyon1.fr/software/seaview.html

They are also available as packages of most Linux distributions.

These programs should be put in your PATH or in the same directory as the seaview

executable for seaview to drive them.

By default seaview searches for the phyml executable under the names PhyML-3.1_linux32

or PhyML-3.1_linux64. If they are installed under other names on your system, seaview 

will ask you for their name and location which are remembered for subsequent runs.

<?xml version="1.0" encoding="UTF-8"?>

<!-- Copyright 2015 Manolo Gouy <manolo.gouy_at_univ-lyon1.fr> -->

<component type="desktop">

 <id>seaview.desktop</id>

 <metadata_license>CC0-1.0</metadata_license>

 <project_license>GPL-3.0</project_license>

 <name>SeaView</name>

 <summary>GUI for multiple sequence alignment and molecular phylogeny</summary>

 <description>

<p>SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.</p>

<ul>

	<li>SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP,

	MASE, Newick) of DNA and protein sequences and of phylogenetic trees.</li>

	<li>SeaView drives programs muscle or Clustal-Omega for multiple sequence alignment, 

	and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.</li>

	<li>Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.</li>

	<li>SeaView computes phylogenetic trees by:</li>

	<li>- parsimony, using PHYLIP's dnapars/protpars algorithm,</li>

	<li>- distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,</li>

	<li>- maximum likelihood, driving program PhyML 3.1.</li>

	<li>SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.</li>

	<li>SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.</li>

</ul>

 </description>

 <screenshots>

  <screenshot type="default">

   <image>http://doua.prabi.fr/binaries/seaview4.png</image>

   <caption>The main alignment window used in the color-by-codon mode</caption>

  </screenshot>

  <screenshot>

   <image>http://doua.prabi.fr/binaries/seaview-tree.png</image>

   <caption>The tree window with some zoom-in applied</caption>

  </screenshot>

  <screenshot>

   <image>  http://doua.prabi.fr/software/seaview_data/PhyML-dialog.png</image>

   <caption>Dialog window to perform Maximum-Likelihood tree-building</caption>

  </screenshot>

 </screenshots>

 <url type="homepage">http://doua.prabi.fr/software/seaview</url>

 <updatecontact>manolo.gouy_at_univ-lyon1.fr</updatecontact>

 <developer_name>Manolo Gouy</developer_name>

  <keywords>

  <keyword>molecular phylogeny</keyword>

  <keyword>phylogenetic tree</keyword>

  <keyword>sequence alignment</keyword>

  <keyword>parsimony</keyword>

  <keyword>neighbor-joining/keyword>

  <keyword>maximum likelihood</keyword>

  </keywords>

</component>

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.</a> 

Comput. Appl. Biosci., 12:543-548.

<p>

Version 4.6.5

Version 4.7

<p>Binaries and full source code available from <a href=http://doua.prabi.fr/software/seaview>http://doua.prabi.fr/software/seaview</a>

<p>Seaview drives the Muscle, Clustal Omega, Gblocks, and PhyML programs and uses code from the PHYLIP

package for parsimony. Please quote:

<ul><li>Edgar R.C. (2004) <a href=http://dx.doi.org/10.1093/nar/gkh340>MUSCLE: multiple sequence alignment with high accuracy and 

    high throughput.</a> Nucleic Acids Res. 32(5):1792-1797.

    high throughput.</a> <i>Nucleic Acids Res.</i> 32(5):1792-1797.

<li>Sievers F. et al. (2011) <a href=http://dx.doi.org/10.1038/msb.2011.75>Fast, scalable generation of high-quality protein 

multiple sequence alignments using Clustal Omega.</a>

    Molecular Systems Biology 7:539.

    <i>Molecular Systems Biology</i> 7:539.

<li>Castresana J. (2000) <a href=http://mbe.oxfordjournals.org/content/17/4/540.full>Selection of conserved blocks from multiple alignments for their 

  use in phylogenetic analysis.</a> Molecular Biology and Evolution 17(4):540-552. 

  use in phylogenetic analysis.</a> <i>Molecular Biology and Evolution</i> 17(4):540-552.

<li>Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. (2010) 

  <a href=http://dx.doi.org/10.1093/sysbio/syq010>New Algorithms and Methods to Estimate Maximum-Likelihood 

  Phylogenies: Assessing the Performance of PhyML 3.0</a>. Systematic Biology 59(3):307-321.

  Phylogenies: Assessing the Performance of PhyML 3.0</a>. <i>Systematic Biology</i> 59(3):307-321.

<li>Felsenstein J. (2013) <a href=http://evolution.genetics.washington.edu/phylip.html>PHYLIP</a> version 3.696.

<li>Lemoine F., Domelevo Entfellner J.-B., Wilkinson E., Correia D., Dávila Felipe M., De Oliveira T. & Gascuel O. (2018) <a href=http://dx.doi.org/10.1038/s41586-018-0043-0>Renewing Felsenstein’s phylogenetic bootstrap in the era of big data.</a> <i>Nature</i> 556:452-456.

</ul>

Seaview uses the <a href=http://www.fltk.org>FLTK</a> project for its user interface.

  <br><u> ignore all gap sites:</u> if on, all gap-containing sites are excluded from analysis;

      if off, not all sequence pairs use the same set of sites for computation of distances.

  <br><u> Bootstrap:</u> performs bootstrap evaluation of clade statistical support (can be interrupted).

  Bootstrap supports can be optionally computed with the <a href=https://doi.org/10.1038/s41586-018-0043-0>Transfer Bootstrap Expectation</a> method.

  Furthermore, if "Show bootstrap trees" is checked,

  individual bootstrap trees will appear in a second tree window, in addition to the main distance tree window.

  <br><u> User tree:</u> computes least squares branch lengths for selected user tree topology.

Systematic Biology 59(3):307-321. 

 <br><u>   Model:</u> select one among a variety of evolutionary models.

 <br><u>   Branch support:</u> can be omitted (None) or estimated either by the approximate likelihood 

       ratio test approach (aLRT) or by bootstrap. In the last case, if "Show bootstrap trees" is checked,

       individual bootstrap trees will appear in a second tree window, in addition to the main PhyML tree window.

 ratio test approach (aLRT) or by bootstrap. The bootstrap branch support can be computed by

 two methods:

 <ul><li> The 'standard' method (Felsenstein's) counts the fraction of replicates containing each internal

   branch of the reference tree.

   <li> The 'Transfer Bootstrap Expectation' method (TBE) proposed by Lemoine <i>et al.</i>:

     <a href=https://doi.org/10.1038/s41586-018-0043-0>Renewing Felsenstein’s phylogenetic bootstrap in the era of big data</a>.

     </ul>

 If "Transfer Bootstrap Expectation method" is checked, both methods for computing

 bootstrap supports are used and displayed in two tree windows.

 With both bootstrap methods, if "Show bootstrap trees" is checked,

 individual bootstrap trees will appear in yet another tree window.

 <br><u> Nucleotide/Amino acid equilibrium frequencies:</u> Residue frequencies can be estimated by counting

 their frequencies in the sequence alignment ("Empirical" option). Alternatively, they can be optimized by 

 maximum likelihood ("Optimized" option for DNA data) or fixed to a set of model-given values ("Model-given"