Sequence Alignment and Phylogenetic Tree Construction of Malarial Parasites

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is ...

A New Alignment Free Method for Phylogenetic Tree Construction

In this paper various methods of sequence analysis which include the alignment based and alignment free methods of tree generation are reviewed and these find distance/similarity among the sequences of different species. Alignment free method based on tuple count and set theory is proposed and the results are compared with the guide tree obtained using alignment based method. The proposed metho...

SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models

MOTIVATION Aligning multiple proteins based on sequence information alone is challenging if sequence identity is low or there is a significant degree of structural divergence. We present a novel algorithm (SATCHMO) that is designed to address this challenge. SATCHMO simultaneously constructs a tree and a set of multiple sequence alignments, one for each internal node of the tree. The alignment ...

Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models

We present a new algorithm (SATCHMO) that simultaneously estimates a tree and generates a set of multiple sequence alignments given a set of protein sequences. Alignments are constructed for each node in the tree. These alignments predict the structurally conserved elements of the sequences in a subtree and are therefore of different lengths, and represent different amino acid preferences, at d...

Malarial Fevers and Malarial Parasites