DOI: 10.5281/zenodo.4285788
title: SequenceBouncer Example Datafiles

description: SequenceBouncer Example datafile information: 1a_mammalian_mtDNA_unaligned.fasta : Mammalian mtDNAs downloaded from the RefSeq database, with duplicates removed. 1b_mammalian_mtDNA_input_alignment.fasta : The input alignment of mammalian mtDNAs that was subjected to SequenceBouncer analysis. 1c_mammalian_mtDNA_full_analysis_cleaned_alignment.fasta : The cleaned alignment resulting from SequenceBouncer full analysis of aligned mammalian mtDNA at k 1.75 and a gap threshold of 2%. 1d_mammalian_mtDNA_full_analysis_rejected_alignment.fasta : The rejected sequences resulting from SequenceBouncer full analysis of aligned mammalian mtDNA at k 1.75 and a gap threshold of 2%. 1e_mammalian_mtDNA_full_analysis_nCS_table.csv : The normalized comparison score table generated during a full analysis of aligned mammalian mtDNA sequences at a gap threshold of 2%. 1f_mammalian_mtDNA_full_analysis_output.csv : Retention or rejection decisions for each mammalian mtDNA sequence entry at k 1.75 and a gap threshold of 2%. 1g_mammalian_mtDNA_full_analysis_cleaned_and_realigned.fasta : Realigned 1c_mammalian_mtDNA_full_analysis_cleaned_alignment.fasta. __ 2a_bird_COI-5P_barcodes_unaligned.fasta : COI-5P barcodes for class Aves downloaded from BOLD, with duplicates removed. 2b_bird_COI-5P_barcodes_input_alignment.fasta : The input alignment of bird COI-5P barcodes that was subjected to SequenceBouncer analysis. 2c_bird_COI-5P_barcodes_full_analysis_cleaned_alignment.fasta : The cleaned alignment resulting from SequenceBouncer full analysis of aligned bird COI-5P barcodes at k 1 and a gap threshold of 5%. 2d_bird_COI-5P_barcodes_full_analysis_rejected_alignment.fasta : The rejected sequences resulting from SequenceBouncer full analysis of aligned bird COI-5P barcodes at k 1 and a gap threshold of 5%. 2e_bird_COI-5P_barcodes_full_analysis_nCS_table.csv.zip : The normalized comparison score table generated during a full analysis of aligned bird COI-5P barcodes at a gap threshold of 5% (compressed to ZIP). 2f_bird_COI_5P_barcodes_full_analysis_output.csv : Retention or rejection decisions for each bird COI-5P barcode at k 1 and a gap threshold of 5%. 2g_bird_COI_5P_barcodes_full_analysis_cleaned_and_realigned.fasta : Realigned 2c_bird_COI-5P_barcodes_full_analysis_cleaned_alignment.fasta 2h_bird_COI-5P_barcodes_sampling_analysis_cleaned_alignment.fasta : The cleaned alignment resulting from SequenceBouncer sampling-based analysis of aligned bird COI-5P barcodes at k 1, a gap threshold of 5%, moderate stringency, sample size of 100, and 10 trials. 2i_bird_COI-5P_barcodes_sampling_analysis_rejected_alignment.fasta : The rejected sequences resulting from SequenceBouncer sampling-based analysis of aligned bird COI-5P barcodes at k 1, a gap threshold of 5%, moderate stringency, sample size of 100, and 10 trials. 2j_bird_COI-5P_barcodes_sampling_analysis_output.csv : Retention or rejection decisions for each bird COI-5P barcode at k 1, a gap threshold of 5%, moderate stringency, sample size of 100, and 10 trials. __ 3a_COVID-19_unaligned.fasta : COVID-19 sequences downloaded from the RefSeq database (compressed to ZIP). 3b_COVID-19_input_alignment.fasta : The input alignment of COVID-19 sequences that was subjected to SequenceBouncer analysis (compressed to ZIP). 3c_COVID-19_sampling_analysis_cleaned_alignment_S1.fasta : The cleaned alignment resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, minimal stringency, sample size of 100, and 10 trials (compressed to ZIP). 3d_COVID-19_sampling_analysis_rejected_alignment_S1.fasta : The rejected sequences resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, minimal stringency, sample size of 100, and 10 trials (compressed to ZIP). 3e_COVID-19_sampling_analysis_cleaned_alignment_S2.fasta : The cleaned alignment resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, moderate stringency, sample size of 100, and 10 trials (compressed to ZIP). 3f_COVID-19_sampling_analysis_rejected_alignment_S2.fasta : The rejected sequences resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, moderate stringency, sample size of 100, and 10 trials (compressed to ZIP). 3g_COVID-19_sampling_analysis_cleaned_alignment_S3.fasta : The cleaned alignment resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, maximum stringency, sample size of 100, and 10 trials (compressed to ZIP). 3h_COVID-19_sampling_analysis_rejected_alignment_S3.fasta : The rejected sequences resulting from SequenceBouncer sampling-based analysis of aligned COVID-19 sequences at k 1, a gap threshold of 2%, maximum stringency, sample size of 100, and 10 trials (compressed to ZIP). 3i_COVID-19_sampling_analysis_cleaned_and_realigned_S1.fasta : Realigned 3c_COVID-19_sampling_analysis_cleaned_alignment_S1.fasta (compressed to ZIP). 3j_COVID-19_sampling_analysis_cleaned_and_realigned_S2.fasta : Realigned 3e_COVID-19_sampling_analysis_cleaned_alignment_S2.fasta (compressed to ZIP). 3k_COVID-19_sampling_analysis_cleaned_and_realigned_S3.fasta : Realigned 3g_COVID-19_sampling_analysis_cleaned_alignment_S3.fasta (compressed to ZIP).