Alignments

ClustalX

ClustalX is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.

Reference: J.D. Thompson et al. (1997). Nucleic Acids Research 24: 4876-4882.

VennPlex

VennPlex - a program that illustrates the often diverse numerical interactions among multiple, high-complexity datasets, using up to four data sets. VennPlex includes versatile output features, where grouped data points in specific regions can be easily exported into a spreadsheet. This program is able to facilitate the analysis of two to four gene sets and their corresponding expression values in a user-friendly manner.

Reference: Cai H et al. (2013) PLoS One; 8(1): e53388.

BioEdit

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by Tom Hall (North Carolina State University). It also provides BLAST capability on local databases.

CHROMA

CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic). The formatted annotation can be sent directly into Microsoft Word, or saved to a file or Windows Clipboard in both HTML and "Rich Text" Formats.

Reference: L. Goodstadt & C.P. Ponting. (2001) Bioinformatics 17: 845-846.

SeaView

SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows ones to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally improve the alignment.

Sequence Demarcation Tool

Sequence Demarcation Tool (SDTv1.2) is a free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results. The identity scores are calculated as 1-(M/N) where M is the number of mismatching nucleotides and N the total number of positions along the alignment at which neither sequence has a gap character.

Reference: Muhire BM et al. (2014) PLoS ONE 9(9): e108277.