Table of Contents

1. Introduction
2. Publications Supplementary Data
   1. SATCHMO-JS: A webserver for simultaneous protein multiple sequence alignment and tree construction
3. Resources

Introduction

SATCHMO stands for Simultaneous Alignment and Tree Construction using Hidden Markov Models. The original algorithm used all-vs-all HMM-HMM scoring and alignment to co-estimate a phylogenetic tree and multiple sequence alignment for protein sequences [1]. This gave SATCHMO robustness to handling highly variable sequences, but made it computationally too expensive to apply to large datasets. SATCHMO-JS is an extension of the SATCHMO algorithm and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-vs-all HMM-HMM scoring and alignment.

Publications Supplementary Data

Reference cited:

1. Edgar, R., and Sjölander, K., "SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models," Bioinformatics. 2003 Jul 22;19(11):1404-11.

Resources

• SATCHMO-JS Webserver
• Original SATCHMO Webserver
• Berkeley Phylogenomics Group Website