First commit. Major update from the previous version. Some new functionality has been added as well as the code has been improved and also some bugs have been fixed

Author: scapella

AUTHORS

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+** Authors **
+
+Salvador Capella-Gutierrez.
+  Comparative Genomics Group. Bioinformatics and Genomics Department.
+  Centre for Genomic Regulation. Barcelona, Spain.
+  e-mail: scapella _at_ crg.es
+
+Toni Gabaldón.
+  Comparative Genomics Group. Bioinformatics and Genomics Department.
+  Centre for Genomic Regulation. Barcelona, Spain.
+  e-mail: tgabaldon _at_ crg.es
+
+** Authors (until trimAl v1.1) **
+
+Jose Ma. Silla-Martínez.
+  e-mail: josilma1 _at_ gmail.com

CHANGELOG

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+trimAl/readAl v1.2. April 2009.
+
+  * Added the htmlout to track the trimAl's trimming.
+
+  * Added the possibility to delete spurious sequences from the alignment.
+
+  * Added the complementary and colnumbering options.
+
+  * Added the manual selection of columns.
+
+  * Added one new heuristic method to select the best automated trimming method.
+    * Automated1
+
+  * Added two new automated methods to work with gaps and similarity distribution.
+    * Strict
+    * Strictplus
+
+  * Select only one automated method to work with gaps distribution.
+    * Strict => Gappyout
+    * Relaxed was deleted
+
+  * Added the version/revisions system.
+
+  * Improved the file format.
+    * Added support for phylip 3.2
+    * Added support for clustal
+    * Added support for fasta
+    * Added support for nexus
+    * Added support for mega
+    * Added support for nbrf/pir
+
+  * Improved of statistics methods. 
+    * Improved the information of the available methods.
+    * Added the identity statistics.
+
+  * Improved of windows size methods. 
+    * Consistency windows size.
+
+  * Improved the similarity-matrices handling.
+
+  * Improved the support for DNA/RNA alignments.
+
+  * Added readAl.
+
+  * Fixed some bugs from the previous version.
+
+trimAl v1.1. February 2008.
+
+  * Initial public version of trimAl.

LICENSE

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+Basic Installation
+==================
+
+The simplest way to compile this package is:
+
+  1. 'cd' to the directory containing the package's source code ('source').
+
+  2. Type 'make' to compile the package.
+
+  3. Optionally, run trimAl/readAl with the examples into the 'dataset' 
+     directory to check the correct installation.
+
+   By default, 'make' compiles the source code of trimAl and readAl in the
+current directory. After that, you can either add to PATH the current
+directory or move these files to '/usr/local/bin' or to '/usr/bin' using
+root privileges.