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## Output directory and overview <a name="output_directory"></a>
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If no output directory has been set using the `--output` flag, then the folder that contains the input alignments is used as the output directory. If a non-existant directory has been provided, then that directory and all of its parent directories are automatically created. All CSV files uses a semicolon, `;`, as a field separator. After running this program, the following files are generated:
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If no output directory has been set using the `--output` flag, then the folder that contains the input alignments is used as the output directory. If a non-existant directory has been provided, then that directory and all of its parent directories are automatically created. All CSV files uses a comma, `,`, as a field separator. After running this program, the following files are generated:
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```
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<output directory>/
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## Supermatrix statistics <a name="summary_statistics"></a>
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This file contains statistics of all input and output alignments, treated as a single concatenated alignment. Supermatrix statistics are stored to the `supermatrix_stats.csv` file and uses a semicolon (';') as a field separator. If jackknifing was performed, results will be included here, but none of the alignments will be saved.
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This file contains statistics of all input and output alignments, treated as a single concatenated alignment. Supermatrix statistics are stored to the `supermatrix_stats.csv` file and uses a comma (',') as a field separator. If jackknifing was performed, results will be included here, but none of the alignments will be saved.
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Missing data is calculated by counting the number of gap characters (gap characters recognized by PhyloPyPruner are '-', '?' or 'x') for each sequence as well as multiplying the alignment length by the number of OTUs that are missing from it. This is done per alignment and the summary of missing data for each alignment is then divided by the total number of alignments. For display purposes, this number is rounded and multiplied by 100.
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### Input alignment statistics <a name="homolog_statistics"></a>
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Statistics for each _individual_ input alignment are stored into `output_alignment_stats.csv`, using a semicolon (';') as a field separator.
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Statistics for each _individual_ input alignment are stored into `output_alignment_stats.csv`, using a comma (',') as a field separator.
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**Table.** Example of an input alignment statistics file.
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## Output alignment statistics <a name="ortholog_statistics"></a>
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Statistics for each _individual_ output alignment are stored into `output_alignment_stats.csv`, using a semicolon (';') as a field separator. The following is an example of what such a file might look like.
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Statistics for each _individual_ output alignment are stored into `output_alignment_stats.csv`, using a comma (',') as a field separator. The following is an example of what such a file might look like.
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**Table.** Example of an output alignment statistics file.
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