Pairwise (EMBOSS)

pairwise is an EMBOSS program that does needle pairwise alignments of sequences from a file of sequences, where every sequence is aligned with every other sequence. This helps speed up doing pairwise alignments for large numbers of sequences by reducing the I/O and program starting overheads.

Because this can take up a lot of space very quickly, you might also want to use an alignment compression system.

To use pairwise with EMBOSS, download the EMBOSS source and this file: emboss_pairwise.zip. Unzip the file in the EMBOSS source directory and follow the instructions in PAIRWISE_README to modify the emboss/Makefile.am file before compiling with:

./configure
make

pairwise is similar to needle with a few exceptions:

• -asequence now expects a file containing multiple sequences. Each sequence is aligned with all of the sequences coming after it in the file, so order will affect the output.
• -start and -end will start the pairwise alignment and stop the pairwise alignment according to the position of sequences in the file (i.e., 200 to 400). This allows the pairwise alignments to be broken up in portions that can be distributed to a cluster computer.