Fundamentals of Bioinformatics - Ogurtsov, A.N. 2013

Methods of Bioinformatics Analysis
Phylogenetic Analysis
Tools for Phylogenetic Analysis

PAUP and PHYLIP are universal tools designed for phylogenetic analysis.

The PAUP (Phylogenetic Analysis Using Parsimony) phylogenetic analysis software incorporates as many diverse Functions (including graphical tree display) as any single independent, platform-agnostic program with a menu-driven interface can offer.

Class="center">http://paup.csit.fsu.edu/.

The PHYLIP (PHYLogeny Inference Package) software suite consists of approximately 30 programs that address the majority of phylogenetic analysis tasks.

http://evolution.genctics.washington.edu/phylip.html.

This command-line interface software does not support mouse input and relies on direct command typing.

The PALI (Phylogeny and ALIgnment of homologous protein structures) database contains sequence alignments generated from spatial structures, alongside Structure-based phylogenetic trees of homologous domains belonging to Protein Families.

http://pali.mbu.iisc.emct.in/index.html.

Phylogenetic relationships are represented using Two Types of tree diagrams (based on sequences):

1) a diagram constructed using a structural dissimilarity metric defined for pairwise alignments;

2) a diagram (structure-based) constructed from similarity data of topologically equivalent residues.

The SUPFAM database contains potential relationships among superfamily members, inferred by comparing structure-grouped families with sequence-grouped families.

http://supfam.mbu.iisc.ernet.in/index.html.

Semi-automatic Databases include the PASS2 (Protein Alignment organized as Structural Superfamilies) database.

http://caps.nebs.res.in/pass2/.

METABOLISM/35.html">Selection/41.html">Review Questions and Assignments

1. What does Homology mean?

2. How does homology differ from similarity?

3. Which genes are called orthologs?

4. Which homologous sequences are called paralogs?

5. WHAT IS A phylogenetic scheme?

6. What is phylogeny?

7. What is phenetics?

8. What is cladistics?

9. What is clustering?

10. What is a clade?

11. What is The Essence of the cladistic maximum parsimony method?

12. What is the essence of the cladistic maximum likelihood method?

13. How does variable evolutionary rate affect the results of phylogenetic analysis?



Last update: 11/08/2026

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