Madina Rasulova Molecular Systematics of Nematodes Page 1
Madina Rasulova Molecular Systematics of Nematodes Page 1 Madina Rasulova Molecular Systematics of Nematodes Page 1
that it was found just by chance, consequently, the more significant) and maximum identity (stands for the maximum similarities shown in percentages, the higher the percentage – the more identical sequences). BLAST can be used to infer functional and evolutionary relationships between sequences as well as help to identify members of gene families. Clustal is a widely used computer program for multiple sequence alignment (Thompson et al., 1997) existing mainly in two variations: ClustalW and ClustalX. The former has a command line interface, while the latter has a graphical user interface. Clustal gives a possibility to perform a global-multiple sequence alignment by the progressive method. The process consists of three main steps: (1) implementation of a pairwise alignment; (2) creation of a phylogenetic tree (or use a user-defined tree); (3) usage of the phylogenetic tree to carry out a multiple alignment. GenDoc is a software for carrying out editing processes of multiple sequence alignment as well as its visualization and analysis. It is very convenient to use this program manual editing of sequence alignment and prepare it for publication because of easy-to-use point as well as click user interface with extensive keyboard mapping. Forcon makes it easy to convert alignment files from one format into other, so converting formats used by all popular software packages for sequence alignment and phylogenetic tree inference. Forcon is able to convert files from CLUSTAL, EMBL, FASTA, GCG/MSF, Hennig86, MEGA, NBRF/PIR, Parsimony Jackknifer, PAUP/NEXUS, PHYLIP and TREECON to any of mentioned above formats. PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for inferring and interpreting phylogenetic trees. It analyzes molecular sequences data using maximum likelihood, parsimony and distance methods. An extensive selection of analysis options and model choices are included into PAUP*. Besides, it accommodates DNA, RNA, protein and general data types. The rich array of options for dealing with phylogenetic trees including importing, combining, comparing, Madina Rasulova Molecular Systematics of Nematodes Page 6
constraining, rooting and testing hypotheses makes this program very attractive to use (Wilgenbusch and Swofford, 2003). MrBayes is a program for the Bayesian inference of phylogeny, which is based on the posterior probability distribution of trees. This probability is the probability of a tree conditioned on the observations, executed using Bayes's theorem. Since it is not possible to calculate the posterior probability distribution of trees analytically, the principle of MrBayes is based on usage of a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. TreeView is a simple, but very useful program for displaying and manipulating phylogenetic trees. It gives a possibility to view the contents of such format tree file as NEXUS, PHYLIP, Hennig86, Clustal and others. It is very convenient to run several tree files just in one TreeView and compare the trees obtained from different programs as well as create publication quality trees. The chosen 13 sequences from BLAST of nucleotides were saved as a “fasta” file format and multiple sequence alignment was performed by the help of the program ClustalX v.1.8 which resulted in a new file “PROJECT_seq.aln” (Appendix, Figure 5). For editing processes GenDoc 2.5 was used and a file “PROJECT_GenDoc.rtf” was generated in which it was possible to find out the total length of sequences as well as variation. Next, the previously obtained file was converted into Nexus format using the program ForCon, in fact the “PROJECT.pau” file was generated. This program was several times edited by the help of notepad and additional commands were typed in the end of the file (Appendix, Figure 6) for performing phylogenetic analysis using such programs as PAUP* 4.0 and MrBayes. The program PAUP* 4.0 resulted in such files as “PROJECT_MP.tre” and “PROJECT_MP.txt” for maximum parsimony method, “PROJECT_NJ.tre” and “PROJECT_NJ.txt” for minimum evolution (neighbor-joining) method, “PROJECT_ML.tre” and “PROJECT_ML.txt” for maximum likelihood method, and “PROJECT_distance.txt” for distance analysis. After, the program MrBayes was used in order to generate Madina Rasulova Molecular Systematics of Nematodes Page 7
- Page 1 and 2: Madina Rasulova Molecular Systemati
- Page 3 and 4: very sandy soils and are active whe
- Page 5: level analyses because of appreciab
- Page 9 and 10: 2 DQ672373 Belonolaimus longicaudat
- Page 11 and 12: of other species of the same genus
- Page 13 and 14: ermudagrass (Poteet) isolates were
- Page 15 and 16: outside of Florida are reproductive
- Page 17 and 18: Han H-R., Jeyaprakash A., Weingarth
- Page 19 and 20: APPENDIX Figure 4. Results of BLAST
- Page 21 and 22: Figure 7. NJ, MP and ML trees with
- Page 23 and 24: Figure 9. Phylogenetic tree MP. Max
- Page 25: Figure 11. Phylogenetic tree MrB. B
that it was found just by chance, consequently, the more significant) and maximum identity (stands<br />
for the maximum similarities shown in percentages, the higher the percentage – the more identical<br />
sequences). BLAST can be used to infer functional and evolutionary relationships between sequences<br />
as well as help to identify members <strong>of</strong> gene families.<br />
Clustal is a widely used computer program for multiple sequence alignment (Thompson et al., 1997)<br />
existing mainly in two variations: ClustalW and ClustalX. The former has a command line interface,<br />
while the latter has a graphical user interface. Clustal gives a possibility to perform a global-multiple<br />
sequence alignment by the progressive method. The process consists <strong>of</strong> three main steps: (1)<br />
implementation <strong>of</strong> a pairwise alignment; (2) creation <strong>of</strong> a phylogenetic tree (or use a user-defined<br />
tree); (3) usage <strong>of</strong> the phylogenetic tree to carry out a multiple alignment.<br />
GenDoc is a s<strong>of</strong>tware for carrying out editing processes <strong>of</strong> multiple sequence alignment as well as its<br />
visualization and analysis. It is very convenient to use this program manual editing <strong>of</strong> sequence<br />
alignment and prepare it for publication because <strong>of</strong> easy-to-use point as well as click user interface<br />
with extensive keyboard mapping.<br />
Forcon makes it easy to convert alignment files from one format into other, so converting formats<br />
used by all popular s<strong>of</strong>tware packages for sequence alignment and phylogenetic tree inference.<br />
Forcon is able to convert files from CLUSTAL, EMBL, FASTA, GCG/MSF, Hennig86, MEGA,<br />
NBRF/PIR, Parsimony Jackknifer, PAUP/NEXUS, PHYLIP and TREECON to any <strong>of</strong> mentioned<br />
above formats.<br />
PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for inferring<br />
and interpreting phylogenetic trees. It analyzes molecular sequences data using maximum likelihood,<br />
parsimony and distance methods. An extensive selection <strong>of</strong> analysis options and model choices are<br />
included into PAUP*. Besides, it accommodates DNA, RNA, protein and general data types. The rich<br />
array <strong>of</strong> options for dealing with phylogenetic trees including importing, combining, comparing,<br />
<strong>Madina</strong> <strong>Rasulova</strong> <strong>Molecular</strong> <strong>Systematics</strong> <strong>of</strong> <strong>Nematodes</strong> <strong>Page</strong> 6
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