ANCESCON is a package for distance-based phylogenetic inference and reconstruction of ancestral protein
sequences that takes into account the observed variation of evolutionary rates between positions that
more precisely describes the evolution of protein families.
[Reconstruction of ancestral protein sequences and its applications, Wei Cai, Jimin Pei, and Nick V Grishin
BMC Evol Biol. 2004; 4: 33. doi: 10.1186/1471-2148-4-33. Published online 2004 September 17.]
Cluster a set of unaligned FASTA sequences by single-linkage clustering
A clustering is performed based on all against all BLAST similarities and the detected groups are returned. Only BLAST similarities better
than a specified cutoff are used to perform the cluster analysis.
Alternatively, the results can be displayed in a more interactive manner using the program CLANS (available for download HERE )
ClubSub-P is a database of cluster-based subcellular localization (SCL) predictions for Archaea and Gram negative bacteria. It combines existing feature prediction and SCL prediction tools into a consensus prediction pipeline. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false positive and false negative predictions.
domain annotation in Trimeric Autotransporter Adhesins
GCView extracts and displays the genomic context of protein coding genes found in homology searches. It is possible to combine multiple queries to visualize conserved genomic neighborhood or operon structure of protein coding genes.
HHcluster is a tool that allows users to explore the galaxy of protein folds. The galaxy was constructed by an all-against-all HMM-HMM comparison of all protein domains in SCOP 1.75 filtered by 20% sequence identity and a subsequent clustering step with CLANS.
NEIGHBOR is a program of the PHYLIP package for inferring phylogenies. Based on a sequence alignment (DNA or Protein) this tool computes two phylogenetic trees, using Neighbor Joining and UPGMA. Trees are displayed in PostScript and ASCII format. Additionally bootstrapping in conjunction with consensus tree evaluation can be enabled.