
Plenty of scripts there ... but not all of them are useful !
Here follows the list of scripts that have been removed.
This list aims at keeping an historical record in case those files are needed one day.

* scripts/hcr/

     scripts/hcr/CleanLSFHeaders.pl
     scripts/hcr/README
     scripts/hcr/subsetAxtFromAndToCompara.pl
     scripts/hcr/tight.mat

This folder used to contain a script to extract the alignments of highly-conserved regions

tags: HCR, axt, 34 bp minimum length, 3400 minimum score


* scripts/misc/
     scripts/misc/ConvertChimpCoordsScaffold2Chromosome.pl
     scripts/misc/all.agp

Script to concert the coordinates on scaffolds to coordinates on chromosomes, following an AGP file

tags: AGP, coordinates, assembly, scaffolds, chromosomes, chimpanzee


* dumps/DumpAndLoadConstrainedElements.pl

Was used to transfer constrained-elements from a pre-53 database to a post-53 database


* scripts/production/create_mlss_table*
    scripts/production/create_mlss_table.conf
    scripts/production/create_mlss_table.pl

Script to generate an HTML table with the list of all the alignments that are in the database.
This list is now dynamically generated by the webcode, so we don't need to keep the script around.


* scripts/pipeline/comparaLoadOrtheus.pl

Script used to run the output of Ortheus back in the days when there was no eHive pipeline to do this.

* scripts/taxonomy/mysqldumpGenomeDBNcbiTaxa.pl

This was used when the ncbi_taxa_* tables had the pruned taxonomy. This is not needed any more since
we keep the whole taxonomy there

* scripts/das/* and modules/Bio/Das/ProServer/SourceAdaptor/*

Modules and scripts used to provide a DAS server out of a Compara database. DAS has been retired

* scripts/homology/InsertParaloguesPrediction.pl + comparaDirectLoadHomology.pl + transfer_homologies.pl

They've been used in very old releases to load homology data into a Compara database

* scripts/view_alignment

This directory used to contain scripts to fetch Compara alignment and format them to be used
in the Staden software suite

* scripts/pipeline/prune_tree.pl

Used at some point to load the species-tree in the EPO-2X pipeline. Now replaced with the MakeSpeciesTree runnable

* scripts/pipeline/dump_genomes2fasta.pl

Replaced with "standaloneJob.pl Bio::EnsEMBL::Compara::Production::EPOanchors::DumpGenomeSequence"

* scripts/dumps/DumpChromosomeFragments.pl

Removed. Used to dump a genome by splitting each chromosome into chunks

* scripts/dumps/DumpConservationScores.pl

Removed. Replaced by the DumpConservationScores_conf pipeline
