The 16S rRNA sequences of isolates were multiple aligned using the ClustalW algorithm.
Sequence alignment was performed using the ClustalW algorithm as part of Megalign (DNASTAR Inc., Madison, WI, USA) and modified.
The full-length cDNA sequences were aligned first using the ClustalW algorithm in Mega 3.1 [3.1.
Multiple sequence alignments were built with Vector NTi (invitrogen) using the ClustalW algorithm and edited by hand [52].
We then aligned each group of 100 sequences using the ClustalW algorithm in the Mega 3.1 software package [35].
Sequences were aligned without gaps using the ClustalW algorithm [22] and collapsed into haplotypes using TCS v.1.21 [23].
All sequences were edited with reference to chromatograms and aligned in MEGA v4 [25] using the ClustalW algorithm [26].
Deduced amino acid sequences were then obtained from TIGR and/or GenBank (http://www.ncbi.nlm.nih.gov/) and aligned using the ClustalW algorithm (http://npsa-pbil.ibcp.fr/).ibcp.fr/
In a second step, a multiple sequence alignment was performed using the clustalw algorithm of the bioedit software with default settings, and then manually corrected [39], [40].
Clusters of TARs and sequence homologs were aligned using the CLUSTALW algorithm to generate multiple sequence alignment blocks suited for RNAz analysis [44].
Amino acid homology between paralogs of Avr1a or alleles of Avr3a was determined using the ClustalW algorithm at default parameters using the MegAlign module.
