Merge pull request #420 from ryneches/master

Fix some broken URLs

Author: bqminh

README.md

@@ -32,9 +32,9 @@ Key features of IQ-TREE
 
 The strength of IQ-TREE is the availability of a wide variety of phylogenetic models:
 
-* __Common models__: All [common substitution models](http://www.iqtree.org/doc/Substitution-Models) for DNA, protein, codon, binary and morphological data with [rate heterogeneity among sites](http://www.iqtree.org/doc/Substitution-Models/#rate-heterogeneity-across-sites) and [ascertainment bias correction](http://www.iqtree.org/doc/Substitution-Models/#ascertainment-bias-correction) for e.g. SNP data.
+* __Common models__: All [common substitution models](http://www.iqtree.org/doc/Substitution-Models) for DNA, protein, codon, binary and morphological data with [rate heterogeneity among sites](http://www.iqtree.org/doc/Substitution-Models#rate-heterogeneity-across-sites) and [ascertainment bias correction](http://www.iqtree.org/doc/Substitution-Models#ascertainment-bias-correction) for e.g. SNP data.
 * __[Partition models](http://www.iqtree.org/doc/Complex-Models/#partition-models)__: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.
-* __Mixture Models__: [fully customizable mixture models](http://www.iqtree.org/doc/Complex-Models/#mixture-models) and [empirical protein mixture models](http://www.iqtree.org/doc/Substitution-Models/#protein-models) and.
+* __Mixture Models__: [fully customizable mixture models](http://www.iqtree.org/doc/Complex-Models#mixture-models) and [empirical protein mixture models](http://www.iqtree.org/doc/Substitution-Models#protein-models) and.
 * __Polymorphism-aware models (PoMo)__: <http://www.iqtree.org/doc/Polymorphism-Aware-Models>
 
 

doc/html/md__r_e_a_d_m_e.html

@@ -82,9 +82,9 @@ <h1><a class="anchor" id="autotoc_md1"></a>
 </ul>
 <p >The strength of IQ-TREE is the availability of a wide variety of phylogenetic models:</p>
 <ul>
-<li><b>Common models</b>: All <a href="http://www.iqtree.org/doc/Substitution-Models">common substitution models</a> for DNA, protein, codon, binary and morphological data with <a href="http://www.iqtree.org/doc/Substitution-Models/#rate-heterogeneity-across-sites">rate heterogeneity among sites</a> and <a href="http://www.iqtree.org/doc/Substitution-Models/#ascertainment-bias-correction">ascertainment bias correction</a> for e.g. SNP data.</li>
-<li><b><a href="http://www.iqtree.org/doc/Complex-Models/#partition-models">Partition models</a></b>: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.</li>
-<li><b>Mixture Models</b>: <a href="http://www.iqtree.org/doc/Complex-Models/#mixture-models">fully customizable mixture models</a> and <a href="http://www.iqtree.org/doc/Substitution-Models/#protein-models">empirical protein mixture models</a> and.</li>
+<li><b>Common models</b>: All <a href="http://www.iqtree.org/doc/Substitution-Models">common substitution models</a> for DNA, protein, codon, binary and morphological data with <a href="http://www.iqtree.org/doc/Substitution-Models#rate-heterogeneity-across-sites">rate heterogeneity among sites</a> and <a href="http://www.iqtree.org/doc/Substitution-Models#ascertainment-bias-correction">ascertainment bias correction</a> for e.g. SNP data.</li>
+<li><b><a href="http://www.iqtree.org/doc/Complex-Models#partition-models">Partition models</a></b>: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.</li>
+<li><b>Mixture Models</b>: <a href="http://www.iqtree.org/doc/Complex-Models#mixture-models">fully customizable mixture models</a> and <a href="http://www.iqtree.org/doc/Substitution-Models#protein-models">empirical protein mixture models</a> and.</li>
 <li><b>Polymorphism-aware models (PoMo)</b>: <a href="http://www.iqtree.org/doc/Polymorphism-Aware-Models">http://www.iqtree.org/doc/Polymorphism-Aware-Models</a></li>
 </ul>
 <h1><a class="anchor" id="autotoc_md2"></a>

doc/latex/md__r_e_a_d_m_e.tex

@@ -16,9 +16,9 @@
 
 
 \begin{DoxyItemize}
-\item {\bfseries{Common models}}\+: All \href{http://www.iqtree.org/doc/Substitution-Models}{\texttt{ common substitution models}} for DNA, protein, codon, binary and morphological data with \href{http://www.iqtree.org/doc/Substitution-Models/\#rate-heterogeneity-across-sites}{\texttt{ rate heterogeneity among sites}} and \href{http://www.iqtree.org/doc/Substitution-Models/\#ascertainment-bias-correction}{\texttt{ ascertainment bias correction}} for e.\+g. SNP data.
-\item {\bfseries{\href{http://www.iqtree.org/doc/Complex-Models/\#partition-models}{\texttt{ Partition models}}}}\+: Allowing individual models for different genomic loci (e.\+g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.
-\item {\bfseries{Mixture Models}}\+: \href{http://www.iqtree.org/doc/Complex-Models/\#mixture-models}{\texttt{ fully customizable mixture models}} and \href{http://www.iqtree.org/doc/Substitution-Models/\#protein-models}{\texttt{ empirical protein mixture models}} and.
+\item {\bfseries{Common models}}\+: All \href{http://www.iqtree.org/doc/Substitution-Models}{\texttt{ common substitution models}} for DNA, protein, codon, binary and morphological data with \href{http://www.iqtree.org/doc/Substitution-Models\#rate-heterogeneity-across-sites}{\texttt{ rate heterogeneity among sites}} and \href{http://www.iqtree.org/doc/Substitution-Models\#ascertainment-bias-correction}{\texttt{ ascertainment bias correction}} for e.\+g. SNP data.
+\item {\bfseries{\href{http://www.iqtree.org/doc/Complex-Models\#partition-models}{\texttt{ Partition models}}}}\+: Allowing individual models for different genomic loci (e.\+g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.
+\item {\bfseries{Mixture Models}}\+: \href{http://www.iqtree.org/doc/Complex-Models\#mixture-models}{\texttt{ fully customizable mixture models}} and \href{http://www.iqtree.org/doc/Substitution-Models\#protein-models}{\texttt{ empirical protein mixture models}} and.
 \item {\bfseries{Polymorphism-\/aware models (Po\+Mo)}}\+: \href{http://www.iqtree.org/doc/Polymorphism-Aware-Models}{\texttt{ http\+://www.\+iqtree.\+org/doc/\+Polymorphism-\/\+Aware-\/\+Models}}
 \end{DoxyItemize}\hypertarget{md__r_e_a_d_m_e_autotoc_md2}{}\doxysection{IQ-\/\+TREE web service}\label{md__r_e_a_d_m_e_autotoc_md2}
 For a quick start you can also try the IQ-\/\+TREE web server, which performs online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at
@@ -72,4 +72,4 @@
 \end{DoxyItemize}\hypertarget{md__r_e_a_d_m_e_autotoc_md5}{}\doxysubsubsection{Credits and Acknowledgements}\label{md__r_e_a_d_m_e_autotoc_md5}
 Some parts of the code were taken from the following packages/libraries\+: \href{http://www.libpll.org}{\texttt{ Phylogenetic likelihood library}}, \href{http://www.tree-puzzle.de}{\texttt{ TREE-\/\+PUZZLE}}, \href{http://dx.doi.org/10.1093/oxfordjournals.molbev.a025808}{\texttt{ BIONJ}}, \href{http://dx.doi.org/10.1093/bioinformatics/btg319}{\texttt{ Nexus Class Libary}}, \href{http://eigen.tuxfamily.org/}{\texttt{ Eigen library}}, \href{http://www.sprng.org}{\texttt{ SPRNG library}}, \href{http://www.zlib.net}{\texttt{ Zlib library}}, \href{http://www.cs.unc.edu/Research/compgeom/gzstream/}{\texttt{ gzstream library}}, \href{http://www.agner.org/optimize/}{\texttt{ vectorclass library}}, \href{https://www.gnu.org/software/gsl/}{\texttt{ GNU scientific library}}.
 
-IQ-\/\+TREE was partially funded by the \href{http://www.fwf.ac.at/}{\texttt{ Austrian Science Fund -\/ FWF}} (grant no. I 760-\/B17 from 2012-\/2015 and and I 2508-\/B29 from 2016-\/2019) and the \href{https://www.univie.ac.at/}{\texttt{ University of Vienna}} (Initiativkolleg I059-\/N). 
+IQ-\/\+TREE was partially funded by the \href{http://www.fwf.ac.at/}{\texttt{ Austrian Science Fund -\/ FWF}} (grant no. I 760-\/B17 from 2012-\/2015 and and I 2508-\/B29 from 2016-\/2019) and the \href{https://www.univie.ac.at/}{\texttt{ University of Vienna}} (Initiativkolleg I059-\/N). 

utils/tools.cpp

@@ -5969,7 +5969,7 @@ void usage_alisim(){
     << "                            users should specify the seed number" << endl
     << "  -gz                       Enable output compression but taking longer running time" << endl
     << "  -af phy|fasta             Set the output format (default: phylip)" << endl
-    << "  User Manual is available at http://www.iqtree.org/doc/alisim" << endl;
+    << "  User Manual is available at http://www.iqtree.org/doc/AliSim" << endl;
 }
 
 void usage_iqtree(char* argv[], bool full_command) {