Clustal X is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.

You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.

Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.

Clustal X has two modes which can be selected using the switch directly above the sequence display: MULTIPLE ALIGNMENT MODE and PROFILE ALIGNMENT MODE.

To do a MULTIPLE ALIGNMENT on a set of sequences, make sure MULTIPLE ALIGNMENT MODE is selected. A single sequence data area is then displayed. The ALIGNMENT menu then allows you to either produce a guide tree for the alignment, or to do a multiple alignment following the guide tree, or to do a full multiple alignment.

In PROFILE ALIGNMENT MODE, two sequence data areas are displayed, allowing you to align 2 alignments (termed profiles). Profiles are also used to add a new sequence to an old alignment, or to use secondary structure to guide the alignment process. GAPS in the old alignments are indicated using the "-" character. PROFILES can be input in ANY of the allowed formats; just use "-" (or "." for MSF/RSF) for each gap position. In Profile Alignment Mode, a button "Lock Scroll" is displayed which allows you to scroll the two profiles together using a single scroll bar. When the Lock Scroll is turned off, the two profiles can be scrolled independently.