Computational Systems Biology Methods and Protocols.7z

3.2.3 CLUSTAL Clustal is an effective tool for multiple alignment of nucleic acid and
protein sequences. After downloading the software, we input data
containing DNA sequences, then set certain parameters and wait
for the results. When multiple sequence alignment is needed, we
use Clustal X.
The proper input formats conclude NBRF/PIR, FASTA,
EMBL/Swiss-Prot, Clustal, GCC/MSF, GCG9 RSF, and GDE,
while the output format can be Clustal, NBRF/PIR, GCG/MSF,
PHYLIP, GDE, or NEXUS.
When using Clustal for data analysis, the bigger the input file is,
the longer it takes for alignment. The results obtained from Clustal
can be further utilized by loading the output file into other software
like MEGA, which will be soon discussed.

1. Download the desktop application and open it.


2. Upload file containing DNA sequences in proper format; at
   this stage, you can have a look at the colored bases.


3. Select different tools for different purposes:
   Select “do complete alignment” for a pairwise alignment.
   Select “do alignment from guide tree and phylogeny” to create
   a guide tree (or use a user-defined tree).
   Select “produce guide tree only” to use the guide tree to carry
   out a multiple alignment.


4. Review the results, save it in a favorable format.


5. The results can be used for further studies.

3.2.4 MEGA MEGA is short for Molecular Evolutionary Genetics Analysis. As a
desktop application released in 1993, it has continuously helped
users conduct statistical analysis of biological macromolecules to
study molecular evolution and construct phylogenetic trees [8].
MEGA is multifunctional. In addition to sequence alignment
construction, it performs outstandingly in distance estimation and
tree-making. To be more precise, the fact that MEGA has included
likelihood methods for estimating evolutionary distances between
sequence pairs as well as distance-based and maximum parsimony
methods for inferring phylogenetic trees is historical.

1. Download the desktop application MEGA and open it.


2. Upload file containing DNA sequences in proper format, or
   open a file conducted by Clustal or any other tools that have
   results MEGA can recognize and further analyze.


3. Click “do complete alignment” if you upload DNA sequences;
   otherwise skip this step.


4. Select tools like “compare pairwise distances” or “construct
   neighbor-joining tree” for certain purposes.


5. Save the results in required format.

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