📄️ Introduction
PyPI version
📄️ Alignment Concatenation
Steps
📄️ Alignment Conversion
Convert an alignment from one format to another format. Optimized for converting many alignments in parallel without the limitation for Python's GIL.
📄️ Alignment Filtering
Filter an alignments. Available filtering options:
📄️ Alignment Partition Conversion
Convert alignment partition data between different formats. Available partition formats:
📄️ Alignment Splitting
Split an alignment into multiple alignments based on partition information.
📄️ Alignment Summary
Generate summary statistics for DNA and amino acid alignments.
📄️ Genomic Summary
Genomic summary statistics is available for FASTQ reads and contiguous sequences.
📄️ Sequence Extraction
Extract sequences based on the sequence ID. Available methods:
📄️ Sequence ID Extraction & Mapping
Extract unique sequence IDs from a collection of alignments and map them to the corresponding loci.
📄️ Sequence Removal
Remove sequences based on the sequence ID. It is the opposite of sequence extraction. It is faster when the sequence to be removed is less than a half of the total sequences. Available methods:
📄️ Sequence Translation
Translate nucleotide sequences to amino acid sequences. For available translation tables, see CLI translation guideline. Note that the translation table is in a string format, not an integer.