Nucleotide sequences of protein-coding genes were aligned based upon amino-acid alignments using CodonAlign [75].
The DNA sequences were aligned based on the protein alignment.
Nucleotide sequences were aligned based on amino acid alignments using MUSCLE 3.6 [ 88].
The nucleotide sequences were aligned based on amino acid alignment using PRANK by applying the TranslatorX perl script [ 43].
The protein-coding DNA sequences were aligned based on their protein alignments at the web server http://www.bork.embl.de/pal2nal/[ 27].
Nucleotide sequences of selected subgroups of Rab proteins were aligned based on corresponding amino acid alignments.
All PCGs were aligned based on amino acid sequence alignments in MEGA version 4.0 [ 41].
Thereafter, the nucleotide sequences were aligned based on the protein sequence alignment profile using PAL2NAL [ 61].
Prank [ 80] was used to conduct codon alignment, in which two protein sequences were aligned first and then DNA sequences were aligned based on the corresponding protein alignments.
The codons were aligned based upon their aligned amino acid sequences, and these alignments were used to infer tree topologies using the neighbor joining method.
The remainder of the sequences is then aligned based on the consistency constraints given by these pre-aligned positions.
