https://github.com/jorvis/ergatis
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Tip revision: 124aafc15b3022a85103a2f3a6a0b7e82a5dc4bf authored by Shaun Adkins on 04 January 2023, 15:16:46 UTC
fixed perl path
Tip revision: 124aafc
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454_mplex_seq_bin_trim
RAPSearch2
RNAmmer
SPAdes
aat_aa
aat_aa_masked
aat_na
aat_na_masked
adjust_bsml_coordinates
alien_hunter
align_bowtie_stats
align_tophat_split_stats
align_tophat_stats
amoscmp
antigenic
aragorn
assert_disjoint_clusters
assign_dbxref_ids
augustus
auto_annotate
auto_gene_curation
backupdb
bam2bigwig
bam2coverage
bam2sam
bam_merge
basic_alignment_stats
bcpconverter
bepipred
ber
blast2go
blast2lca
blast_lgt_finder
blast_seq_screen
blast_snp_regions
blastn_plus
blastp_plus
bmtagger
bmtagger_index
bowtie
bowtie_build
bsml2chado
bsml2fasta
bsml2featurerelationships
bsml2gff3
bsml2interevidence_fasta
bsml2mugsymap
bsml2ptt
bsml2tbl
bsml_qc
btab2taxon
bulk_delete_chado
bwa
bwa_mem
celera-assembler
celera2hawkeye
chado2bsml
chado2flatfile
chado_report_pages
clean_fasta
cleanse_sgc_database
clovr_16S_rdptables
clovr_metagenomics_prep
clovr_metagenomics_tables
clustalw
cluster_mapping
combine_ncRNA_alignments
complete_study_stage
concatenate_files
condor_cogs_search
coords_to_glimmer3
core_qiime
create_amoscmp_input
create_cuffsuite_files
create_db_list_file
create_map_file
create_paired_list_file
create_pseudomolecules
crossbow
cuffcompare
cuffdiff
cuffdiff_filter
cufflinks
cummerbund
curate_common_names
cvtermpath_closure
db2bsml
db2fasta
delete_bcp
delete_by_bcp
deseq
download_sra
download_tcga
drop_chado_indexes
dump_fasta
dump_table
edgeR
elph
error_detector
exonerate
expression_plots
extract_assembly_stats
extract_snp_regions
fast_tree
fasta2bsml
fastaToBsmlWorkingGeneModels
fastortho
fastq_to_CA
fastqc_stats
fastx_quality_stats
fastx_toolkit
fastx_trimming
fetch_genbank
fgenesh
filter_bogus_genes
filter_deseq
filter_dups_lc_seqs
filter_fastq
filter_lgt_class_a_genes
filter_lgt_class_b_genes
filter_lgt_class_c_genes
filter_merged_table
filter_sequences_by_id
find_homopolymers
fix_gene_symbols
formatdb
formatdb_snp
fuzznuc
genbank2bsml
genbank2fasta
genbank2gff3
genbank2gtf
geneid
genemark
genemark-es
genewise
genezilla
genscan
genscan-plus
get_bam_coverage_dx
getorf
gff3_to_annotab
gff3_to_fasta
gff3_to_gbrowse
gkpstore2fastq
glimmer3
glimmerHMM
glk2bsml
gsnap
histogram_stacked
hmmer
hmmls
hmmpfam
hmmpfam3
htseq
htseq_count_reads
identify_human_contaminants
infernal
initdb
insert_pmarks_in_scaffolds
intergenic_analysis
iprscan
islandpath
j_ortholog_clusters
jaccard
ksnp
leech
legacy2bsml
lgt_build_bwa_index
lgt_bwa
lgt_bwa_fq
lgt_bwa_post_process
lgt_create_validated_bam
lgt_mpileup
lipop
lipoprotein_motif
load_ber_for_manatee
make_circleator_figure
make_comparative_circleator_figure
make_snp_lists
map_snp_query_pos
mask_by_analysis
megablast
metagene
metagenemark
metastats
mosaik
mothur_align_seqs
mothur_chimera_slayer
mothur_classify_seqs
mothur_cluster
mothur_collect_single
mothur_dist_seqs
mothur_filter_seqs
mothur_get_oturep
mothur_rarefaction_single
mothur_read_otu
mothur_screen_seqs
mothur_summary
mothur_tree_shared
mothur_trim_seqs
mothur_unique_seq_limit
mothur_unique_seqs
move_to_scratch
mpileup
mugsy_callsnps
mugsy_concat_fasta
mugsyalign
mugsycog
mugsyprep
mumi-reduce
mummer
mumsgraph
muscle
ncbi-blastall
ncbi-blastn
ncbi-blastn_compress
ncbi-blastp
ncbi-blastx
ncbi-tblastn
ncbi-tblastx
ngap
nucmer
nucmer-delta-filter
nucmer-show-snps
nucmer-snp2merged
nucmer_snps
obo2chado
open_reading_frames
order_paired_list
outer_membrane_domain
overlap_analysis
p_func
paired_iterator
paired_list_iterator_template
pangenome_blast_parse
pangenome_do_analysis
pangenome_fix_headers
pangenome_make_graphs
pangenome_make_pangenome
pangenome_make_profile
pangenome_make_table
pangenome_merge_results
panther
parallel_sort
parse_evidence
parse_for_ncRNA
parse_for_ncRNAs
parse_mpileup_for_positions
pathway_tools_input
pepstats
percent_gc
percent_mapped_stats
phage_finder
phat
phobos
phylip_dnadist
pick_otus_through_otu_table
piecharts
pileup_to_wig
pipeline_summary
pmarks2bsml
predict_operons
predict_prokaryotic_gene_function
predotar
prepare_paired_ends_for_velvet
preserve_reads_in_fastq
priam_ec_assignment
prodigal
profile_bsml
profile_gff3
prok_pipeline_check
prokpipe_consistency_checks
promote_gene_prediction
ps_scan
pseudomolecule2glimmer3
psiblast
psortb
qiime_fasta_mothur_cnvr
qiime_fastq_mothur_cnvr
quicktree
rdp_classifier
refresh_chado_mart
remove_db_gene_syms_with_hypos
remove_indices_and_constraints
remove_subset_of_gis
repeatmasker
replace_defline_with_locusID
resistome
restore_indices_and_constraints
restoredb
rotate_molecule
rpkm_coverage_stats
rpsblast
rrna_hmm_fs
run_command
run_workflow
runsql
sam2bam
sam2fasta
sam2lca
samtools_alignment_stats
samtools_file_convert
samtools_merge
samtools_reference_index
scp_files
scripture
seg
selfsim
sff_to_CA
sfffile
sffinfo
shared
sighunt
signalp
skiff
snap
snp-add-gene-info
snp_verify
soapdenovo
solsnp
sort_sam_by_name
split_fasta
split_fasta_fastq
split_fastq
split_file
split_multifasta
split_paired_files
sra2fastq
stap_aligner
stap_classifier
start_site_curation
summarize_mugsy_comparative_pipeline
tRNAscan-SE
tRNAscan-SE_compress
tabula_rasa
tag_data
targetp
tbl2asn
tblastn_plus
tmhmm
tophat
train_for_glimmer3_iteration
translate_sequence
trf
truncate_chado_mart
uchime
uclust
uclust_remove_replicates
update_ec_numbers
update_euk_model_sequences
usearch
validate_asn
validate_bsml
validate_chado_records
validate_euk_records
validate_fasta
validate_genbank
validate_gff3
validate_sgc_records
velvet
velvet_optimiser
wait
wga_maf2tree
wrapper_align
wu-blastn
wu-blastp
wu-blastx
wu-tblastn
xdformat

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