├── .gitignore ├── COPYRIGHT ├── COPYRIGHT.sse2 ├── FASTA_LIST ├── LICENSE ├── README ├── README.md ├── bin └── README ├── conf ├── README ├── fast_libs_e.www ├── fast_new └── fastlibs ├── data ├── README.md ├── VTML_10.mat ├── VTML_120.mat ├── VTML_160.mat ├── VTML_20.mat ├── VTML_200.mat ├── VTML_40.mat ├── VTML_80.mat ├── blosum45.mat ├── blosum50.mat ├── blosum62.mat ├── blosum80.mat ├── dna.mat ├── idn_aa.mat ├── md_10.mat ├── md_20.mat ├── md_40.mat ├── optima5.mat ├── pam120.mat ├── pam250.mat ├── rna.mat └── vtml160.mat ├── doc ├── INSTALL ├── README.versions ├── README_sql.md ├── README_v36.3.8d.md ├── README_v36.3.8i.md ├── changes_v34.html ├── changes_v35.html ├── changes_v36.html ├── fasta.defaults ├── fasta.history.tex ├── fasta.options ├── fasta36.1 ├── fasta_func.doc ├── fasta_guide.bib ├── fasta_guide.fg1.tex ├── fasta_guide.fg2.tex ├── fasta_guide.pdf ├── fasta_guide.tex ├── fasta_versions.html ├── fastf3.1 ├── fasts3.1 ├── map_db.1 ├── prss3.1 ├── ps_lav.1 ├── readme.md ├── readme.v30 ├── readme.v30t6 ├── readme.v30t7 ├── readme.v31t0 ├── readme.v31t1 ├── readme.v32t0 ├── readme.v33t0 ├── readme.v34t0 ├── readme.v35 ├── readme.v36 └── readme.w32 ├── make ├── Makefile ├── Makefile.NetBSD ├── Makefile.cray_pvp ├── Makefile.fcom ├── Makefile.freebsd ├── Makefile.hpux_it ├── Makefile.ibm ├── Makefile.linux ├── Makefile.linux32 ├── Makefile.linux32_simde_arm ├── Makefile.linux32_sse2 ├── Makefile.linux64 ├── Makefile.linux64_simde_arm ├── Makefile.linux64_sse2 ├── Makefile.linux_icc ├── Makefile.linux_icc_sse2 ├── Makefile.linux_mariadb ├── Makefile.linux_mysql ├── Makefile.linux_pgsql ├── Makefile.linux_sql ├── Makefile.linux_sse2 ├── Makefile.mp_com2 ├── Makefile.mpi_icc_sse2 ├── Makefile.nm_fcom ├── Makefile.nm_pcom ├── Makefile.nmk_icl ├── Makefile.os_x ├── Makefile.os_x86 ├── Makefile.os_x86_64 ├── Makefile.os_x86_clang ├── Makefile.os_x86_icc ├── Makefile.os_x_arm64 ├── Makefile.pLinux ├── Makefile.pLinux_sql ├── Makefile.pcom ├── Makefile.pcom_s ├── Makefile.pcom_t ├── Makefile.sgi ├── Makefile.sse_alt ├── Makefile.sun ├── Makefile.sun_x86 ├── Makefile35.common ├── Makefile35.common_sql ├── Makefile35.nmk_com ├── Makefile35m.common_mysql ├── Makefile35m.common_pgsql ├── Makefile35m.common_sql ├── Makefile36.nmk_com ├── Makefile36m.common ├── Makefile36m.common_mariadb ├── Makefile36m.common_pgsql ├── Makefile36mpi.common ├── Makefile36t.common ├── README └── make_osx_univ.sh ├── misc ├── README ├── parse_m9.pl ├── res2R.pl └── shuffle_embed.pl ├── psisearch2 ├── NCBI_all.asn ├── README.md ├── clustal2fasta.pl ├── clustal2fasta.py ├── m89_btop_msa2.pl ├── psisearch2_msa.pl ├── psisearch2_msa.py ├── psisearch2_msa_iter.sh └── psisearch2_msa_iter_bl.sh ├── scripts ├── README ├── README.scripts ├── acc_examples ├── ann_exons_all.pl ├── ann_exons_ens.pl ├── ann_exons_ncbi.pl ├── ann_exons_up_sql.pl ├── ann_exons_up_sql_www.pl ├── ann_exons_up_www.pl ├── ann_feats2ipr.pl ├── ann_feats2ipr_e.pl ├── ann_feats_up_sql.pl ├── ann_feats_up_www2.pl ├── ann_ipr_www.pl ├── ann_pdb_cath.pl ├── ann_pdb_vast.pl ├── ann_pfam30_tmptbl.pl ├── ann_pfam_sql.pl ├── ann_pfam_sql.py ├── ann_pfam_www.pl ├── ann_pfam_www.py ├── ann_pfam_www2.pl ├── ann_script_list ├── ann_upfeats_pfam_www_e.pl ├── annot_blast_btop2.pl ├── annot_blast_btop3.py ├── annot_blast_btop4.py ├── blastp_annot_cmd.sh ├── blastp_cmd.sh ├── color_defs.pl ├── exp_up_ensg.pl ├── expand_links.pl ├── expand_refseq_isoforms.pl ├── expand_uniref50.pl ├── expand_up_isoforms.pl ├── fasta_annot_cmd.sh ├── get_genome_seq.py ├── get_protein.py ├── get_protein_sql.py ├── get_protein_sql_www.py ├── get_refseq.py ├── get_uniprot.py ├── get_up_prot_iso_sql.py ├── lav2plt.pl ├── lavplt_ps.pl ├── lavplt_svg.pl ├── links2sql.pl ├── m8CBl_to_plot2.R ├── m8_btop_msa.pl ├── m9B_btop_msa.pl ├── map_exon_coords.py ├── merge_blast_btab.pl ├── merge_fasta_btab.pl ├── plot_domain2t.cgi ├── relabel_domains.py ├── rename_exons.py ├── summ_domain_ident.pl ├── test_ann_scripts.sh ├── test_py.sh └── up_id2acc.py ├── seq ├── bovgh.seq ├── bovprl.seq ├── dna_test_s.nlib ├── dyr_human.aa ├── egmsmg.aa ├── grou_drome.pseg ├── gst.nlib ├── gst.seq ├── gstm1_human.vaa ├── gstm1b_human.nt ├── gstm1b_human_fs.nt ├── gstt1_drome.aa ├── gtm1_human.aa ├── gtt1_drome.aa ├── h10_human.aa ├── hahu.aa ├── hsgstm1b.gcg ├── hsgstm1b.seq ├── humgstd.seq ├── lcbo.aa ├── m1r.aa ├── m2.aa ├── mchu.aa ├── mgstm1.3nt ├── mgstm1.aa ├── mgstm1.aaa ├── mgstm1.e05 ├── mgstm1.eeq ├── mgstm1.esq ├── mgstm1.gcg ├── mgstm1.lc ├── mgstm1.nt ├── mgstm1.nt1 ├── mgstm1.nt12r ├── mgstm1.nt13 ├── mgstm1.nt13r ├── mgstm1.nt1r ├── mgstm1.nts ├── mgstm1.raa ├── mgstm1.rev ├── mgstm1.seq ├── mgstm1_genclone.seq ├── mgtt2_x.seq ├── ms1.aa ├── mu.lib ├── musplfm.aa ├── mwkw.aa ├── mwrtc1.aa ├── myosin_bp.aa ├── n0.aa ├── n1.aa ├── n2.aa ├── n2_fs.lib ├── n2s.aa ├── n2t.aa ├── n_fs.lib ├── ngt.aa ├── ngts.aa ├── oohu.aa ├── oohu.raa ├── prio_atepa.aa ├── prot_test.lib ├── prot_test.lseg ├── prot_test_s.lseg ├── qrhuld.aa ├── titin_hum.aa ├── titin_hum.seq ├── vav_human.aa ├── xurt8c.aa ├── xurt8c.lc └── xurtg.aa ├── sql ├── README ├── create_seq_demo.sql ├── join_up50.pl ├── mysql_demo1.sql ├── mysql_demo_pv.sql ├── nr_to_sql.pl ├── pirpsd.sql ├── psql_demo.sql ├── psql_demo1.sql └── psql_demo_pv.sql ├── src ├── a_mark.h ├── aamap.h ├── ag_stats.c ├── aln_structs.h ├── alt_parms.h ├── altlib.h ├── apam.c ├── best_stats.h ├── build_ares.c ├── c_dispn.c ├── cal_cons.c ├── cal_cons2.c ├── cal_consf.c ├── comp_lib9.c ├── compacc2.c ├── compacc2e.c ├── dec_pthr_subs.c ├── dec_pthr_subs.h ├── defs.h ├── doinit.c ├── drop_func.h ├── dropff2.c ├── dropfs2.c ├── dropfx.c ├── dropfx2.c ├── dropfz2.c ├── dropfz3.c ├── dropgsw2.c ├── dropgsw2.h ├── dropnfa.c ├── dropnfa.h ├── dropnnw2.c ├── dropnsw.c ├── dyn_string.h ├── faatran.c ├── getenv.c ├── getopt.c ├── getseq.c ├── global_sse2.c ├── global_sse2.h ├── glocal_sse2.c ├── glocal_sse2.h ├── h_altlib.h ├── htime.c ├── initfa.c ├── karlin.c ├── last_tat.c ├── last_thresh.c ├── lav_defs.h ├── lib_sel.c ├── list_db.c ├── llgetaa.c ├── lsim4.c ├── lsim4.h ├── map_db.c ├── mm_file.h ├── mmgetaa.c ├── mrandom.c ├── msg.h ├── mshowalign2.c ├── mshowbest.c ├── mw.h ├── mysql_lib.c ├── ncbl2_head.h ├── ncbl2_mlib.c ├── ncbl_head.h ├── ncbl_lib.c ├── nmgetlib.c ├── param.h ├── pcomp_bufs.h ├── pcomp_subs2.c ├── pgsql_lib.c ├── print_pssm.c ├── pssm_asn_subs.c ├── pthr_subs.h ├── pthr_subs2.c ├── randtest.c ├── re_getlib.c ├── res_stats.c ├── rstruct.h ├── sc_to_e.c ├── scaleswn.c ├── scaleswt.c ├── showrss.c ├── simde │ ├── COPYING │ ├── README.md │ ├── check.h │ ├── debug-trap.h │ ├── hedley.h │ ├── simde-arch.h │ ├── simde-common.h │ ├── simde-constify.h │ ├── simde-detect-clang.h │ ├── simde-diagnostic.h │ ├── simde-features.h │ ├── simde-math.h │ └── x86 │ │ ├── mmx.h │ │ ├── sse.h │ │ ├── sse2.h │ │ ├── sse3.h │ │ ├── sse4.1.h │ │ ├── sse4.2.h │ │ └── ssse3.h ├── smith_waterman_altivec.c ├── 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