SequenceBouncer Example Datafiles

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.

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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.

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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).