Abstract: A computer software package called ‘FasParser’ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.