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oushujun

add usage

Mar 1, 2025

923ac4c · Mar 1, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
Class_modify_EDTA_intact_gff.py		Class_modify_EDTA_intact_gff.py	move from /util/ to /bin/ and change paths	Aug 8, 2024
Filter_and_format_blast_for_RECON.pl		Filter_and_format_blast_for_RECON.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
RM_summary.pl		RM_summary.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
RMout2bed.pl		RMout2bed.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
TE_Sequence_Ontology.txt		TE_Sequence_Ontology.txt	Hieu Nguyen's contribution	Feb 26, 2025
TE_purifier.pl		TE_purifier.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
TE_sankey_plotter.py		TE_sankey_plotter.py	move from /util/ to /bin/ and change paths	Aug 8, 2024
add_id.pl		add_id.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
bed2gff.pl		bed2gff.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
buildSummary.pl		buildSummary.pl	Update buildSummary.pl	Aug 8, 2024
call_seq_by_list.pl		call_seq_by_list.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
classify_by_lib_RM.pl		classify_by_lib_RM.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
clean_GRF_TIR.pl		clean_GRF_TIR.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_TE.pl		cleanup_TE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_misclas.pl		cleanup_misclas.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_nested.pl		cleanup_nested.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_nested_old.pl		cleanup_nested_old.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_nonTE.pl		cleanup_nonTE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_proteins.pl		cleanup_proteins.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_tandem.pl		cleanup_tandem.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cleanup_uniq.pl		cleanup_uniq.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
combine_RMrows.pl		combine_RMrows.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
combine_overlap.pl		combine_overlap.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
count_base.pl		count_base.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
count_lowercase.pl		count_lowercase.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
count_mask.pl		count_mask.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
count_nested.pl		count_nested.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
count_repeats.pl		count_repeats.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
cut.pl		cut.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
density_plot.R		density_plot.R	Merge remote-tracking branch 'origin/EDTA2' into EDTA2	Nov 25, 2024
density_table.py		density_table.py	move from /util/ to /bin/ and change paths	Aug 8, 2024
div_plot2.R		div_plot2.R	include more plotting categories	Jan 7, 2025
div_table.pl		div_table.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
div_table2.pl		div_table2.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
evaluation.pl		evaluation.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
fffx		fffx	MUSL compiled version for alpine	Aug 7, 2024
filter_DTT.pl		filter_DTT.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
filter_copy_number.pl		filter_copy_number.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
filter_gff3.pl		filter_gff3.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
filter_gff_TIR.pl		filter_gff_TIR.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
filter_helitronscanner.pl		filter_helitronscanner.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
find_flTE.pl		find_flTE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
flanking_filter.pl		flanking_filter.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
format_TElib.pl		format_TElib.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
format_gff3.pl		format_gff3.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
format_helitronscanner_out.pl		format_helitronscanner_out.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
format_intact_gff3.pl		format_intact_gff3.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_consistent_TE.pl		get_consistent_TE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_ext_seq.pl		get_ext_seq.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_frag.pl		get_frag.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_interspersed_consensus.pl		get_interspersed_consensus.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_lib_len.pl		get_lib_len.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_range.pl		get_range.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
get_range2.pl		get_range2.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
gff2RMout.pl		gff2RMout.pl	add usage	Mar 1, 2025
gff2bed.pl		gff2bed.pl	resolve #494 #495	Nov 25, 2024
gff_cmb.pl		gff_cmb.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
keep_nest.pl		keep_nest.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_bed_with_intact.pl		make_bed_with_intact.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_gff3.pl		make_gff3.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_gff3_with_RMout.pl		make_gff3_with_RMout.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_gff3_with_intact.pl		make_gff3_with_intact.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_masked.pl		make_masked.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
make_panTElib.pl		make_panTElib.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
name_code_decode.pl		name_code_decode.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
output_by_list.pl		output_by_list.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
paf2blast6_chunking2_parallel3_ordered_parts.py		paf2blast6_chunking2_parallel3_ordered_parts.py	move from /util/ to /bin/ and change paths	Aug 8, 2024
patch.pl		patch.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
patch_1.8.3_to_1.9.0.pl		patch_1.8.3_to_1.9.0.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
post-processing.sbatch		post-processing.sbatch	move from /util/ to /bin/ and change paths	Aug 8, 2024
print_hist6.py		print_hist6.py	move from /util/ to /bin/ and change paths	Aug 8, 2024
purger.pl		purger.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_LTR.pl		rename_LTR.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_LTR_skim.pl		rename_LTR_skim.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_RM_TE.pl		rename_RM_TE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_TE.pl		rename_TE.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_by_list.pl		rename_by_list.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
rename_tirlearner.pl		rename_tirlearner.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
run_helitron_scanner.sh		run_helitron_scanner.sh	move from /util/ to /bin/ and change paths	Aug 8, 2024
split_overlap.pl		split_overlap.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
substract.pl		substract.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
substract_parallel.pl		substract_parallel.pl	move from /util/ to /bin/ and change paths	Aug 8, 2024
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