In a scan through ~200 journal of virology papers with the search "phylogenetic*" in abstract or title, maximum likelihood was the most popular tree-inference method. closely followed by neighbor-joining and the jukes-cantor model of nucleotide substitution was the most popular from the list screened (see below). Also the command-line only version of clustal; version w was much more popular than the GUI/user-friendly clustalX.
neighbor$joining 137
parsimony 94
likelihood 156
bayesian 26
upgma 9
p-distance 5
jukes-cantor 21
kimura$2-parameter 8
kimura$3-parameter 0
tamura-nei 20
f81 3
hky 13
general$time-reversible 14
dayhoff 13
jtt 6
wag 2
modeltest 17
model$of$nucleotide 17
model$of$protein 3
clustal$x 36
clustal$w 84
