New upstream version 3.3.1+dfsg

List of changes from version 3.3 to 3.3.1 (until May 8th, 2018)

     - new species pisaster (Pisaster ochraceus, ochre starfish)

     - bugfixes of sampling error in intron model and in check of

       frame-compatibility of CDSpart hints without frame

     - new auxiliary program utrrnaseq to find training UTRs

     - new script setStopCodonFreqs.pl

List of changes from version 3.2.3 to 3.3 (until July 11th, 2017)

     - new program ESPOCA to estimate selective pressure on codon alignments

     - gene finding on ancestral genomes is enabled

	rm -f src/makedepend.pl

	rm -r augustus-training

	cd docs/tutorial2015/results; ls | grep -v do.sh | grep -v README | xargs rm; cd -

	rm -r auxprogs/utrrnaseq/input/human-chr19

	rm -r docs/tutorial-cgp/results/cactusout

	make clean all

	make clean

	cd config/species; rm -rf tobacco xeno1 bombus_terrestris{1,3} symsag xenoturbella meara pavar newest elegans maker2_* lizard

%                                                                                                %

%           Gene Prediction with the Command-Line Version of AUGUSTUS                            %

%                                                                                                %

%           Authors: Lizzy Gerischer, Oliver Keller, Stefanie König, Lars Romoth, Mario Stanke   %

%             Mario Stanke                                                                       %

%           Authors: Lizzy Gerischer, Oliver Keller, Stefanie König, Lars Romoth, Katharina Hoff %

%             and Mario Stanke                                                                   %

%             Universitaet Greifswald                                                            %

%             Institut fuer Mathematik und Informatik                                            %

%             17497 Greifswald                                                                   %

%             Fon: +49 3834 864642                                                               %

%             Fon: +49 3834 4204642                                                              %

%             mario.stanke@uni-greifswald.de                                                     %

%                                                                                                %

%             Date: July 11th, 2017                                                              %

%             Date: May 8th, 2018                                                                %

%                                                                                                %

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

              1. INTRODUCTION

              ---------------

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie König

and Lizzy Gerischer. It can be used as an ab initio program, which means it bases its prediction purely on the

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer and Katharina Hoff. It can be used as an ab initio program, which means it bases its prediction purely on the

sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources

such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS

can also predict the genes simultaneously in several aligned genomes (see README-cgp.txt).

  - Nematostella vectensis (Cnidaria)

  - Ciona intestinalis (Chordata)

  - Strongylocentrotus purpuratus (Echinodermata)

  - Pisaster ochraceus (starfish)

The training annotation files of the following species are a courtesy of Jason Stajich (see also http://fungal.genome.duke.edu/): 

Aspergillus fumigatus, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Botrytis cinerea, Candida albicans

1. unpack

>tar -xzf augustus-3.3.tar.gz

>tar -xzf augustus-3.3.1.tar.gz

The tar-archive contains one directory 'augustus-3.3' with the following sub-directories:

The tar-archive contains one directory 'augustus-3.3.1' with the following sub-directories:

bin

src

include

      to your /etc/apt/sources.list, first: 

      deb http://us.archive.ubuntu.com/ubuntu vivid main universe)

Compiling bam2wig requires:

   -htslib

   -bcftools

   -tabix

   -samtools

   For bam2wig, these four packages must be installed from github. An installation via Ubuntu packages is not sufficient.

   See detailed installation & compilation instructions at auxprogs/bam2wig/README.TXT

   Also, the environment variable TOOLDIR (directory in which htslib, bcftools, tabix and samtools reside) must be exported:

   export TOOLDIR=/path/where/dependencies/reside

   Compiling utrrnaseq requires Boost library >Boost_1_49_0.  For Ubuntu e.g. install with

      sudo apt-get install libboost-all-dev

> make

After compilation has finished, the command bin/augustus should be executable and print a usage message.

HS04636	blat2hints	intron		550	650	.	+	.	priority=5; source=mRNA

When two hints or hint groups contradict each other then the hints with the lower priority number

are ignored. This is especially usefull if for a genome several sources of hints are available,

are ignored. This is especially useful if for a genome several sources of hints are available,

where one source should be trusted when in doubt. For example, the rhesus macaque currently has few native ESTs

but human ESTs often also align to rhesus. Giving the hints from native ESTs a higher priority means

that AUGUSTUS uses only them for genes with support by native ESTs and uses the alien EST alignments

	cd filterBam; make;

	cd homGeneMapping; make;

	cd joingenes; make;

	cd bam2wig; make;

	cd utrrnaseq/Debug; make all;

clean:

	cd bam2hints; make clean;

	cd compileSpliceCands; make clean;

	cd filterBam; make clean;

	cd homGeneMapping; make clean;

	cd joingenes; make clean;

	cd bam2wig; make clean;

	cd utrrnaseq/Debug; make clean;