[med-svn] [Git][med-team/sift][upstream] New upstream version 6.2.1+ds
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 20 08:33:40 BST 2026
Andreas Tille pushed to branch upstream at Debian Med / sift
Commits:
d33f1576 by Andreas Tille at 2026-10-20T08:33:46+02:00
New upstream version 6.2.1+ds
- - - - -
689 changed files:
- + INSTALL
- − README
- − README_4.0.3
- VERSION_UPDATE
- − bin/Classify_SNPs_Indels.pl
- − bin/DNA_PROT_SUBROUTINES.pl
- − bin/IntersectFeatures.jar
- − bin/IntersectLocations.sh
- − bin/SIFT_exome_indels.pl
- − bin/SIFT_exome_nssnvs.pl
- bin/SIFT_for_submitting_NCBI_gi_id.csh
- bin/SIFT_for_submitting_fasta_seq.csh
- − bin/SIFT_intersect_cds.pl
- − bin/SIFT_subroutines.pm
- − bin/SNPClassifier/Classify_SNPs.pl
- − bin/SNPClassifier/Extract_Coding_Info.pl
- − bin/SNPClassifier/Manuals/.svn/all-wcprops
- − bin/SNPClassifier/Manuals/.svn/entries
- − bin/SNPClassifier/Manuals/.svn/format
- − bin/SNPClassifier/Manuals/.svn/prop-base/SNP Class Dataflow.vsd.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/SNP Class Hierachy.vsd.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/SNP Classifier Manual.doc.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/SNP_Classifier_Manual_041206.pdf.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/SNP_Classifier_Manual_041206.ps.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/The SNP CSV File Description.doc.svn-base
- − bin/SNPClassifier/Manuals/.svn/prop-base/The SNP CSV File Description.pdf.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/SNP Class Dataflow.vsd.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/SNP Class Hierachy.vsd.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/SNP Classifier Manual.doc.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/SNP_Classifier_Manual_041206.pdf.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/SNP_Classifier_Manual_041206.ps.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/The SNP CSV File Description.doc.svn-base
- − bin/SNPClassifier/Manuals/.svn/text-base/The SNP CSV File Description.pdf.svn-base
- − bin/SNPClassifier/Manuals/SNP Class Dataflow.vsd
- − bin/SNPClassifier/Manuals/SNP Class Hierachy.vsd
- − bin/SNPClassifier/Manuals/SNP Classifier Manual.doc
- − bin/SNPClassifier/Manuals/SNP_Classifier_Manual_041206.pdf
- − bin/SNPClassifier/Manuals/SNP_Classifier_Manual_041206.ps
- − bin/SNPClassifier/Manuals/The SNP CSV File Description.doc
- − bin/SNPClassifier/Manuals/The SNP CSV File Description.pdf
- − bin/choose_seqs_via_psiblastseedmedian
- − bin/clump_output_alignedseq
- − bin/consensus_to_seq
- − bin/detect_indel.pl
- − bin/detect_repeat.pl
- − bin/fastaseqs
- − bin/get_sequences.pl
- − bin/indelfile_to_gff.pl
- − bin/info_on_seqs
- − bin/linux/choose_seqs_via_psiblastseedmedian
- − bin/linux/clump_output_alignedseq
- − bin/linux/consensus_to_seq
- − bin/linux/fastaseqs
- bin/linux/get_sequences.pl
- − bin/linux/info_on_seqs
- − bin/linux/psiblast_res_to_fasta_dbpairwise
- − bin/linux/seqs_from_psiblast_res
- − bin/map_coords_to_bin.pl
- − bin/map_coords_to_bin_indels.pl
- − bin/model_transcript.pl
- bin/perlscripts/get_BLINK_seq.pl
- web/scripts/separate_query_from_database.pl → bin/perlscripts/separate_query_from_database.pl
- − bin/process_alignment
- − bin/psiblast_res_to_fasta_dbpairwise
- − bin/reformat_chrfile.pl
- bin/seqs_chosen_via_median_info.csh
- − bin/seqs_from_psiblast_res
- − bin/seqs_to_matrixweb
- − bin/sift_feed_to_chr_coords_batch.pl
- − bin/snv_db_engine.pl
- − bin/solaris/README
- − bin/solaris/choose_seqs_via_psiblastseedmedian
- − bin/solaris/clump_output_alignedseq
- − bin/solaris/consensus_to_seq
- − bin/solaris/fastaseqs
- − bin/solaris/info_on_seqs
- − bin/solaris/psiblast_res_to_fasta_dbpairwise
- − bin/solaris/seqs_from_psiblast_res
- + blimps/LAMA.h
- + blimps/Makefile
- + blimps/Makefile.am
- + blimps/Makefile.in
- − blimps/README
- + blimps/aabet.h
- + blimps/alphabet.h
- + blimps/blastapp.h
- + blimps/blimps-mem.c
- + blimps/blimps-mem.h
- + blimps/blimps.c
- + blimps/blimps.h
- + blimps/blkvblk.h
- + blimps/blockmap.h
- + blimps/blocks.c
- + blimps/blocks.h
- + blimps/blocksprogs.h
- + blimps/codehop.h
- + blimps/config.c
- + blimps/config.h
- + blimps/convert.c
- + blimps/convert.h
- + blimps/docs/Makefile.am
- + blimps/docs/Makefile.in
- blimps/docs/coduse.csh
- + blimps/errors.c
- + blimps/errors.h
- + blimps/files.c
- + blimps/files.h
- + blimps/frequency.c
- + blimps/frequency.h
- + blimps/gcode.c
- + blimps/gcode.h
- + blimps/global.h
- + blimps/include/aabet.h
- + blimps/include/alphabet.h
- + blimps/include/blastapp.h
- + blimps/include/blocks.h
- + blimps/include/blocksprogs.h
- + blimps/include/convert.h
- + blimps/include/errors.h
- + blimps/include/files.h
- + blimps/include/frequency.h
- + blimps/include/gcode.h
- + blimps/include/global.h
- web/blocks/license.html → blimps/include/license.h
- + blimps/include/matrix.h
- + blimps/include/memory.h
- + blimps/include/ntbet.h
- + blimps/include/output.h
- + blimps/include/pattern.h
- + blimps/include/protomat.h
- + blimps/include/residues.h
- + blimps/include/sequences.h
- + blimps/include/strutil.h
- + blimps/license.h
- + blimps/lists.c
- + blimps/lists.h
- + blimps/matrix.c
- + blimps/matrix.h
- + blimps/memory.c
- + blimps/memory.h
- + blimps/ntbet.h
- + blimps/obj/blimps-mem.d
- + blimps/obj/blocks.d
- + blimps/obj/config.d
- + blimps/obj/convert.d
- + blimps/obj/errors.d
- + blimps/obj/files.d
- + blimps/obj/frequency.d
- + blimps/obj/gcode.d
- + blimps/obj/lists.d
- + blimps/obj/matrix.d
- + blimps/obj/memory.d
- + blimps/obj/options.d
- + blimps/obj/pattern.d
- + blimps/obj/protomat.d
- + blimps/obj/scores.d
- + blimps/obj/scoring.d
- + blimps/obj/sequences.d
- + blimps/obj/sl.d
- + blimps/obj/strutil.d
- + blimps/obj/version.d
- + blimps/options.c
- + blimps/options.h
- + blimps/output.h
- + blimps/p2c.h
- + blimps/pattern.c
- + blimps/pattern.h
- + blimps/protomat.c
- + blimps/protomat.h
- + blimps/residues.h
- + blimps/scores.c
- + blimps/scores.h
- + blimps/scoring.c
- + blimps/scoring.h
- + blimps/sequences.c
- + blimps/sequences.h
- + blimps/skiplist.h
- + blimps/sl.c
- + blimps/strutil.c
- + blimps/strutil.h
- + blimps/tree.h
- + blimps/version.c
- + blimps/version.h
- − coding_info/Homo_sapien_36
- − coding_info/Homo_sapien_37
- − db/Human_db_36
- − db/repeat_db.gff
- − db/small_indel_errors_ref.gff
- src/Alignment.c
- src/Alignment.h
- src/Array_math.c
- src/Clumping.c
- + src/Clumping.h
- src/List_Number.c
- src/List_Number.h
- src/Matrix_Info.c
- src/Matrix_Info.h
- src/PN_blocks.c
- src/PN_blocks.h
- src/PN_convert.c
- src/PN_convert.h
- src/Protdist.c
- src/Protdist.h
- src/Psiblast.c
- src/Psiblast.h
- src/Psiblast_convert.h
- src/README
- src/SortList.c
- src/SortList.h
- + src/allowed_subst_html.c
- src/blocklist.c
- src/blocklist.h
- src/cccb
- src/choose_seqs_via_psiblastseedmedian.c
- src/clump_output_alignedseq.c
- src/compile.csh
- src/consensus_to_seq.c
- src/info_on_seqs.c
- + src/process_alignment.c
- src/psiblast_res_to_fasta_dbpairwise.c
- src/queue.c
- src/queue.h
- src/seqs_from_psiblast_res.c
- + src/seqs_to_matrixweb.c
- + src/seqs_to_msf.c
- + src/seqs_to_msf_web.c
- src/stringhash.c
- src/stringhash.h
- src/stringlist.c
- src/stringlist.h
- web/sift-bin/NBB1_2 → src/tmp
- − test/indels.input
- + test/lacI.alignedfasta.phr
- + test/lacI.alignedfasta.pin
- + test/lacI.alignedfasta.psq
- + test/lacI.fasta.SIFTprediction
- + test/lacI_db
- + test/lacI_db.phr
- + test/lacI_db.pin
- + test/lacI_db.psq
- − test/snvs.input
- − web/README
- − web/blocks-bin/add_queue_entry.pl
- − web/blocks-bin/addseqs.pl
- − web/blocks-bin/aqe.pl
- − web/blocks-bin/blalign.pl
- − web/blocks-bin/blockmap-testing.pl
- − web/blocks-bin/blockmap.pl
- − web/blocks-bin/bm_format.pl
- − web/blocks-bin/bm_htmlize-map.pl
- − web/blocks-bin/bm_test.pl
- − web/blocks-bin/clean.pl
- − web/blocks-bin/cobbler.pl
- − web/blocks-bin/codehop.pl
- − web/blocks-bin/contact.pl
- − web/blocks-bin/contest.pl
- − web/blocks-bin/cyrcaLama.pl
- − web/blocks-bin/diy.pl
- − web/blocks-bin/format_blocks.pl
- − web/blocks-bin/getblock.pl
- − web/blocks-bin/htmlize-blimps.pl
- − web/blocks-bin/htmlize-blkprob.pl
- − web/blocks-bin/htmlize-blksort.pl
- − web/blocks-bin/htmlize-getblock.pl
- − web/blocks-bin/htmlize-getchrom.pl
- − web/blocks-bin/htmlize-map.pl
- − web/blocks-bin/htmlize-swiss.pl
- − web/blocks-bin/impala.pl
- − web/blocks-bin/junk.pl
- − web/blocks-bin/kidofwais.pl
- − web/blocks-bin/makeblocks.pl
- − web/blocks-bin/narrow.pl
- − web/blocks-bin/nixcheck.pl
- − web/blocks-bin/oligo_melt.pl
- − web/blocks-bin/pdbmast.pl
- − web/blocks-bin/process_blocks.pl
- − web/blocks-bin/rpsblast.pl
- − web/blocks-bin/run_queue.pl
- − web/blocks-bin/test.pl
- − web/blocks-bin/testlib.pl
- − web/blocks-bin/treeviewer.pl
- − web/blocks-bin/tvblock.pl
- − web/blocks/addseqs.html
- − web/blocks/biased_blocks.html
- − web/blocks/biassed_blocks.html
- − web/blocks/blalign.html
- − web/blocks/block_formatter.html
- − web/blocks/blockmap.html
- − web/blocks/blocks_biblio.html
- − web/blocks/blocks_format.html
- − web/blocks/blocks_search.html
- − web/blocks/blocks_tools.html
- − web/blocks/cobbler.html
- − web/blocks/codehop.html
- − web/blocks/contact.html
- − web/blocks/contest.html
- − web/blocks/diy.html
- − web/blocks/getblock.html
- − web/blocks/impala.html
- − web/blocks/index.html
- − web/blocks/make_blocks.html
- − web/blocks/narrow.html
- − web/blocks/oligo_melt.html
- − web/blocks/other.html
- − web/blocks/papers.html
- − web/blocks/process_blocks.html
- − web/blocks/process_test.html
- − web/blocks/rpsblast.html
- − web/blocks/testhop.html
- − web/blocks/thanks.html
- − web/blocks/tvtest.html
- − web/blocks/whats_new.html
- − web/index.html
- − web/scripts/add_organism.pl
- − web/scripts/check_SIFT_BLink.pl
- − web/scripts/check_SIFT_Genome.pl
- − web/scripts/check_SIFT_Seq.pl
- − web/scripts/check_SIFT_dbSNP.pl
- − web/scripts/check_SIFT_indels.pl
- − web/scripts/check_SIFT_pid_subst_all.pl
- − web/scripts/check_toolbox.pl
- − web/scripts/collate_predictions.pl
- − web/scripts/coord.pl
- − web/scripts/dbSNP_parse.pl
- − web/scripts/extract_good_blink.pl
- − web/scripts/extract_selected.pl
- − web/scripts/extract_snps_from_pred_file.pl
- − web/scripts/failure_message.txt
- − web/scripts/flat.txt
- − web/scripts/format_align.pl
- − web/scripts/from_sift/SIFT_prediction.csh
- − web/scripts/from_sift/seqs_chosen_via_median_info_from_list.pl
- − web/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh
- − web/scripts/get_BLINK_grid_seq_batch_ALL.sh
- − web/scripts/get_BLINK_seq.pl
- − web/scripts/get_BLINK_seq_batch.sh
- − web/scripts/get_BLINK_seq_batch_ALL.sh
- − web/scripts/get_BLINK_seq_batch_BEST.sh
- − web/scripts/get_errored_alignedfasta.pl
- − web/scripts/get_first_seq.pl
- − web/scripts/get_median_aln.pl
- − web/scripts/get_median_aln_errored.pl
- − web/scripts/get_median_aln_errored_grid.pl
- − web/scripts/get_median_aln_grid.pl
- − web/scripts/get_median_aln_grid_fast.pl
- − web/scripts/get_sift_prediction.pl
- − web/scripts/get_sift_prediction_errored.pl
- − web/scripts/get_sift_prediction_grid.pl
- − web/scripts/get_validation.pl
- − web/scripts/hack_SIFT_BLink.pl
- − web/scripts/index_alignments.sh
- − web/scripts/index_prediction.sh
- − web/scripts/index_query.sh
- − web/scripts/map_predictions_rsid.pl
- − web/scripts/modify_dbsnp_for_ref.pl
- − web/scripts/modify_index.pl
- − web/scripts/modify_index2.pl
- − web/scripts/muscle.sh
- − web/scripts/out
- − web/scripts/remove.html
- − web/scripts/rename.sh
- − web/scripts/revise_dbsnp.out.pl
- − web/scripts/separate_queries.sh
- − web/scripts/split_for_aligning.pl
- − web/scripts/submitMuscle.sh
- − web/scripts/submitMuscle_batch.sh
- − web/scripts/submitMuscle_batch_partition.sh
- − web/scripts/subst.pl
- − web/scripts/temp.pl
- − web/scripts/test.fasta
- − web/scripts/test.pl
- − web/scripts/verify_ref.pl
- − web/sift-bin/Classify_SNPs.pl
- − web/sift-bin/Classify_SNPs_Indels.pl
- − web/sift-bin/DNA_PROT_SUBROUTINES.pl
- − web/sift-bin/IntersectFeatures.jar
- − web/sift-bin/IntersectLocations.sh
- − web/sift-bin/NBB1_2seq
- − web/sift-bin/NOTES
- − web/sift-bin/PHAT_submission.csh
- − web/sift-bin/PHAT_submission.pl
- − web/sift-bin/PHAT_submission_backup.csh
- − web/sift-bin/PHAT_submission_backup.pl
- − web/sift-bin/PHAT_submission_profile.csh
- − web/sift-bin/PHAT_submission_profile.pl
- − web/sift-bin/SIFT.start.csh
- − web/sift-bin/SIFT.start2.csh
- − web/sift-bin/SIFT2_queue.bak
- − web/sift-bin/SIFTING.csh
- − web/sift-bin/SIFTING2.csh
- − web/sift-bin/SIFTING2.csh.bak
- − web/sift-bin/SIFTING2.csh.orig
- − web/sift-bin/SIFTING2.csh.save
- − web/sift-bin/SIFTING2_Oct15_2004.csh
- − web/sift-bin/SIFTING2_for_subst_only.csh
- − web/sift-bin/SIFTING2_modified_by_pauline.csh
- − web/sift-bin/SIFTING2_old.csh
- − web/sift-bin/SIFT_BLink_submit.pl
- − web/sift-bin/SIFT_BLink_submit.pl.bak
- − web/sift-bin/SIFT_BLink_submit.pl.bkp
- − web/sift-bin/SIFT_BLink_submit_031508.pl
- − web/sift-bin/SIFT_BLink_submit_PNtest.pl
- − web/sift-bin/SIFT_BLink_submit_old.pl
- − web/sift-bin/SIFT_aligned_seqs_submit.pl
- − web/sift-bin/SIFT_aligned_seqs_submit2.pl
- − web/sift-bin/SIFT_aligned_seqs_submitbackup.pl
- − web/sift-bin/SIFT_chr_coords_indels_submit.pl
- − web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl
- − web/sift-bin/SIFT_chr_coords_single_db_submit.pl
- − web/sift-bin/SIFT_chr_coords_submit.pl
- − web/sift-bin/SIFT_chr_coords_submit_012510.pl
- − web/sift-bin/SIFT_chr_coords_submit_020510.pl
- − web/sift-bin/SIFT_chr_coords_submit_030110.pl
- − web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl
- − web/sift-bin/SIFT_chr_coords_submit_bin_query.pl
- − web/sift-bin/SIFT_chr_coords_submit_bkp.pl
- − web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl
- − web/sift-bin/SIFT_chr_coords_submit_in_operator.pl
- − web/sift-bin/SIFT_chr_coords_submit_no_binning.pl
- − web/sift-bin/SIFT_chr_coords_submit_old.pl
- − web/sift-bin/SIFT_chr_coords_submit_prod.pl
- − web/sift-bin/SIFT_chr_coords_submit_refseq.pl
- − web/sift-bin/SIFT_dbSNP_submit.cgi
- − web/sift-bin/SIFT_dbSNP_submit.pl
- − web/sift-bin/SIFT_dbSNP_submit_backup.pl
- − web/sift-bin/SIFT_dbSNP_submit_db.pl
- − web/sift-bin/SIFT_dbSNP_submit_flatfile.pl
- − web/sift-bin/SIFT_feed_to_chr_coords.pl
- − web/sift-bin/SIFT_feed_to_chr_coords_batch.pl
- − web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl
- − web/sift-bin/SIFT_feed_to_chr_coords_check.pl
- − web/sift-bin/SIFT_feed_to_chr_coords_prod.pl
- − web/sift-bin/SIFT_intersect_cds_submit.pl
- − web/sift-bin/SIFT_pid_subst_all_submit.pl
- − web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl
- − web/sift-bin/SIFT_queue
- − web/sift-bin/SIFT_related_seqs_submit.pl
- − web/sift-bin/SIFT_seq_submit.pl
- − web/sift-bin/SIFT_seq_submit2.pl
- − web/sift-bin/SIFT_seq_submit2.pl.bak
- − web/sift-bin/SIFT_seq_submit2.pl.orig
- − web/sift-bin/SIFT_seq_submit2March272004.pl
- − web/sift-bin/SIFT_seq_submit2_121307.pl
- − web/sift-bin/SIFT_seq_submit2_old.pl
- − web/sift-bin/SIFT_seq_submitcopy.pl
- − web/sift-bin/SIFT_software_registration.pl
- − web/sift-bin/SIFT_subroutines.pm
- − web/sift-bin/SIFT_subroutines.pm.bak
- − web/sift-bin/SIFT_subroutines2.pm
- − web/sift-bin/TESTING2.csh
- − web/sift-bin/add_queue_entry.pl
- − web/sift-bin/an_example_of_IP.pl
- − web/sift-bin/catfile.csh
- − web/sift-bin/catfile.sh
- − web/sift-bin/catfile_notitle.csh
- − web/sift-bin/catfilehtml.csh
- − web/sift-bin/clean.csh
- − web/sift-bin/clean.pl
- − web/sift-bin/clean.pl.bak
- − web/sift-bin/clean_am.csh
- − web/sift-bin/clean_hour.csh
- − web/sift-bin/clean_pm.csh
- − web/sift-bin/clean_tmp.csh
- − web/sift-bin/clean_tmp.csh.bak
- − web/sift-bin/clean_up_seq_for_swat.pl
- − web/sift-bin/collate_SIFT_pid_subst.pl
- − web/sift-bin/contact.pl
- − web/sift-bin/contact_old.pl
- − web/sift-bin/default.amino.frq
- − web/sift-bin/detect_indel.pl
- − web/sift-bin/detect_repeat.pl
- − web/sift-bin/detect_repeat3.pl
- − web/sift-bin/email_sift_aatable_results.pl
- − web/sift-bin/error.log
- − web/sift-bin/fastaseqs
- − web/sift-bin/format.pl
- − web/sift-bin/formatdb.log
- − web/sift-bin/gi
- − web/sift-bin/indelfile_to_gff.pl
- − web/sift-bin/index.pl
- − web/sift-bin/lockfile
- − web/sift-bin/logo_nongrouped_web.csh
- − web/sift-bin/logo_web.csh
- − web/sift-bin/logos.csh
- − web/sift-bin/mail_file.pl
- − web/sift-bin/map_choords_to_bin.pl
- − web/sift-bin/map_choords_to_bin_old.pl
- − web/sift-bin/map_choords_to_chr_bin.pl
- − web/sift-bin/map_coords_to_bin_indels.pl
- − web/sift-bin/merge-gff.pl
- − web/sift-bin/model_transcript.pl
- − web/sift-bin/outt
- − web/sift-bin/parse_denormal.pl
- − web/sift-bin/perl.list
- − web/sift-bin/pl.list
- − web/sift-bin/pro_to_prf
- − web/sift-bin/protomat.csh
- − web/sift-bin/protomat_motif.csh
- − web/sift-bin/reformat_chrfile.pl
- − web/sift-bin/restart_queue.sh
- − web/sift-bin/rm.csh
- − web/sift-bin/robots.txt
- − web/sift-bin/run_queue.pl
- − web/sift-bin/seq_to_subfamily_block.csh
- − web/sift-bin/seq_to_subfamily_block.pl
- − web/sift-bin/seq_to_subfamily_block_backup.csh
- − web/sift-bin/seqs_chosen_via_median_info.csh
- − web/sift-bin/sift-bin.tgz
- − web/sift-bin/snpfile_to_gff.pl
- − web/sift-bin/start_queue.sh
- − web/sift-bin/start_queue_as_daemon.pl
- − web/sift-bin/test
- − web/sift-bin/test.pl
- − web/sift-bin/tmp.pl
- − web/sift-bin/write_IP_logfile.pl
- − web/stylesheets/main.css
- − web/tmp
- − web/www/2
- − web/www/CFTR_sprot.html
- − web/www/GR_SIFT_on_dbSNP.pdf
- − web/www/GR_SIFTimplementation.pdf
- − web/www/HIV_alignment.html
- − web/www/HIV_predictiontable.html
- − web/www/HIV_scores.html
- − web/www/IlluminaInterviewFeb2006.pdf
- − web/www/JWB_indels_ncbi36_fixed.txt
- − web/www/JWB_indels_ncbi37_fixed.txt
- − web/www/LacI_SPTRgenomesprob.html
- − web/www/LacI_SPTRprob.html
- − web/www/LacI_alignment_SPTR.html
- − web/www/LacI_alignment_SPTRgenomes.html
- − web/www/Lysozyme_gappedaln.html
- − web/www/PHAT.html
- − web/www/PHAT.pdf
- − web/www/PHAT_help.html
- − web/www/PHAT_paper.pdf
- − web/www/PHAT_profile.html
- − web/www/PHAT_submission.html
- − web/www/SIFT_BLink_submit.html
- − web/www/SIFT_BLink_submit_PNtest.html
- − web/www/SIFT_BLink_submit_old.html
- − web/www/SIFT_BLink_submit_prod.html
- − web/www/SIFT_aligned_seqs_submit.html
- − web/www/SIFT_aligned_seqs_submit2.html
- − web/www/SIFT_aligned_seqs_submit_old.html
- − web/www/SIFT_chr_coords_indels_submit.html
- − web/www/SIFT_chr_coords_indels_submit_old.html
- − web/www/SIFT_chr_coords_submit.html
- − web/www/SIFT_chr_coords_submit_old.html
- − web/www/SIFT_dbSNP.html
- − web/www/SIFT_dbSNP_old.html
- − web/www/SIFT_help.html
- − web/www/SIFT_intersect_coding_submit.html
- − web/www/SIFT_on_blocks.html
- − web/www/SIFT_on_databases/Cargill_WInsSNPs
- − web/www/SIFT_on_databases/Figure_pseudogene.pdf
- − web/www/SIFT_on_databases/Figure_redundantmotif.pdf
- − web/www/SIFT_on_databases/SP/alignedfasta.tar.Z
- − web/www/SIFT_on_databases/SP/prediction.tar.Z
- − web/www/SIFT_on_databases/SP/seq.tar.Z
- − web/www/SIFT_on_databases/Sunyaev_contamination.html
- − web/www/SIFT_on_databases/Table1_references.html
- − web/www/SIFT_on_databases/WhiteheadID.htm
- − web/www/SIFT_on_databases/dbSNP/XP_001.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_001.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_001.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_002.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_002.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_002.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_003.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_003.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_003.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_004.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_004.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_004.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_005.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_005.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_005.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_006.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_006.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_006.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_007.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_007.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_007.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_008.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_008.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_008.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_009.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_009.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_009.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_010.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_010.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_010.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_011.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_011.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_011.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_012.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_012.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_012.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_013.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_013.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_013.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_015.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_015.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_015.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_016.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_016.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_016.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_017.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_017.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_017.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_018.alignedfasta.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_018.predictionscreen.tar.Z
- − web/www/SIFT_on_databases/dbSNP/XP_018.seq.tar.Z
- − web/www/SIFT_on_databases/dbSNP/predictionscreen.tar
- − web/www/SIFT_on_databases/deleterious_snps_screened
- − web/www/SIFT_on_databases/sequence_identical_param.html
- − web/www/SIFT_on_databases/table_sequence_error.html
- − web/www/SIFT_on_databases/tmp
- − web/www/SIFT_on_databases/tmp2
- − web/www/SIFT_pid_subst_all_submit.html
- − web/www/SIFT_pid_subst_all_submit_old.html
- − web/www/SIFT_pid_subst_dbsnp_submit.html
- − web/www/SIFT_pid_subst_submit.html
- − web/www/SIFT_related_seqs_submit.html
- − web/www/SIFT_related_seqs_submit_old.html
- − web/www/SIFT_seq_submit.html
- − web/www/SIFT_seq_submit2.html
- − web/www/SIFT_seq_submit2.html.orig
- − web/www/SIFT_seq_submit2_old.html
- − web/www/SIFTing_databases.html
- − web/www/TEST_seq_submit2.html
- − web/www/about_me.html
- − web/www/annurev.genom.7.080505_SuppTable1.pdf
- − web/www/annurev.genom.7.Ng_Henikoff.pdf
- − web/www/chr7_asian_snps_ncbi37.txt
- − web/www/chr7_snps_on_Asian_genome.txt
- − web/www/chr_coords_example.html
- − web/www/chr_coords_example_indels.html
- − web/www/chr_coords_example_large_files.html
- − web/www/collated_predictions.tsv
- − web/www/collated_predictions_dbSNP.tgz
- − web/www/collated_predictions_dbSNP.tsv
- − web/www/css/homepage.css
- − web/www/css/main.css
- − web/www/cv.html
- − web/www/cvlong.html
- − web/www/do_over
- − web/www/eating_out.html
- − web/www/feinberg.html
- − web/www/formats.html
- − web/www/html.list
- − web/www/hydrophobic_background.html
- − web/www/hydrophobic_form.html
- − web/www/lysozymepred.html
- − web/www/lysozymeprob.html
- − web/www/nprot.2009.86.pdf
- − web/www/phat_paper.pdf
- − web/www/pics/NMD.png
- − web/www/pics/black_oval.GIF
- − web/www/pics/blackpixel.gif
- − web/www/pics/bottomofsifter.GIF
- − web/www/pics/indel_location.png
- − web/www/pics/leftside.gif
- − web/www/pics/new_flash_anim.gif
- − web/www/pics/sifter.GIF
- − web/www/pics/sifter.gif
- − web/www/pics/sifterhandle.GIF
- − web/www/pics/sifterwitharrows.gif
- − web/www/pics/sifterwithstars.gif
- − web/www/pics/tool.gif
- − web/www/pics/wink-2.jpg
- − web/www/pid_all_example.html
- − web/www/pid_dbsnp_example.html
- − web/www/readme_collated_predictions_dbSNP.txt
- − web/www/seq_to_subfamily_block.html
- − web/www/seq_to_subfamily_block_help.html
- − web/www/sift.html
- − web/www/smile.happy.gif
- − web/www/smileyface1.bmp
- − web/www/smileyface2.bmp
- − web/www/smileyface3.bmp
- − web/www/snp_example.txt
- − web/www/snp_help.html
- − web/www/sprot.html
- − web/www/test_sets/HIVproteaseTable.txt
- − web/www/test_sets/LacITable.txt
- − web/www/test_sets/LysozymeTable.txt
- − web/www/transmembrane_prediction.html
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/sift/-/commit/d33f15763648276bda75074102783b0b32f2ac59
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View it on GitLab: https://salsa.debian.org/med-team/sift/-/commit/d33f15763648276bda75074102783b0b32f2ac59
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