GToTree:系统基因组学的用户友好型工作流程
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2021-05-15
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GToTree-master.zip （94个子文件） 
GToTree-master bin 
gtt-parse-assembly-summary-file 2KB gtt-filter-parallel.sh 965B gtt-ncbi-parallel.sh 11KB gtt-store-SCG-HMMs 3KB gtt-pfam-search 54KB gtt-cat-alignments 3KB gtt-hmms 1KB gtt-gen-SCG-HMMs 30KB gtt-genbank-to-AA-seqs 3KB gtt-parse-fasta-by-headers 2KB gtt-fasta-serial.sh 9KB gtt-genbank-parallel.sh 10KB gtt-amino-acid-serial.sh 9KB gtt-parse-gtdb-assembly-summary-file 4KB gtt-fasta-parallel.sh 8KB gtt-genbank-serial.sh 11KB gtt-remove-all-gap-seqs-from-alignment 989B gtt-gen-itol-map 2KB gtt-update-ncbi-taxonomy 517B gtt-ncbi-serial.sh 12KB gtt-append-fasta-headers 1KB gtt-genbank-to-fasta 1KB gtt-get-accessions-from-GTDB 22KB gtt-swap-ids 1KB gtt-get-median.sh 355B gtt-align-and-trim-parallel.sh 3KB gtt-filter-seqs-by-length 1KB gtt-reorder-fasta 1KB gtt-rename-fasta-headers 1KB gtt-check-wanted-lineage-info 1KB gtt-amino-acid-parallel.sh 8KB gtt-clean-after-test.sh 33B gtt-count-bases-per-seq 944B GToTree 177KB gtt-test.sh 1019B ToL_example results ToL_aligned_SCGs_mod_names.faa 3.29MB Genomes_removed_for_too_few_hits.tsv 149B NCBI_genomes_summary_info.tsv 219KB
GToTree_example_ToL_tree.pdf 58KB ToL_aligned_SCGs_mod_names.tre 177KB ToL_all_genomes_summary_info.tsv 375KB ToL_aligned_SCGs.faa 3.18MB GToTree_ToL_accessions 27KB run_log 488B LICENSE 34KB example_run GCF_000011365.1.gbff 18.86MB GCA_002271865.1.fa 4.73MB
alteromonas_refseq_accessions.txt 496B genome_to_id_map.tsv 91B Alteromonas_example Genbank_genomes_summary_info.tsv 221B gtotree-runlog.txt 7KB All_genomes_summary_info.tsv 7KB Aligned_SCGs_mod_names.tre 2KB NCBI_genomes_summary_info.tsv 4KB Aligned_SCGs_mod_names.faa 1.21MB All_genomes_SCG_hit_counts.tsv 13KB Aligned_SCGs.faa 1.21MB Fasta_genomes_summary_info.tsv 146B Genomes_with_questionable_redundancy_estimates.tsv 97B Partitions.txt 5KB run_log.txt 1KB genbank_files.txt 21B fasta_files.txt 19B .gitignore 10B test_data 
GCF_001886455.1_ASM188645v1_protein.faa.gz 811KB test_run_log.txt 370B amino_acid_files.txt 81B fasta_files GCA_000012825.1_ASM1282v1_genomic.fna 4.99MB GCA_000009925.1_ASM992v1_genomic.fna.gz 1.56MB ncbi_accessions.txt 119B GCF_000012505.1_ASM1250v1_genomic.gbff 5.33MB genome_to_id_map.tsv 159B pfam_targets.txt 22B GCA_900473895.1_N32_genomic.gbff.gz 911KB genbank_files.txt 75B GCF_000020585.3_ASM2058v3_protein.faa 1.46MB fasta_files.txt 102B hmm_sets Chlamydiae.hmm 27.61MB Cyanobacteria.hmm 20.86MB Actinobacteria.hmm 10.32MB Firmicutes.hmm 8.48MB Bacteria.hmm 4.76MB Epsilonproteobacteria.hmm 22.44MB Alphaproteobacteria.hmm 8.27MB Archaea.hmm 5.98MB Gammaproteobacteria.hmm 13.63MB Proteobacteria.hmm 8.86MB Bacteroidetes.hmm 6.19MB Universal_Hug_et_al.hmm 939KB Betaproteobacteria.hmm 16.74MB Bacteria_and_Archaea.hmm 1.79MB Tenericutes.hmm 7.68MB hmm_sources_and_info.tsv 43KB README.md 6KB
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