We present a fuzzy technique for approximate k-mer matching that combines the speed of hashing with the sensitivity of dynamic programming. Our approach exploits the collision detection mechanism used by hash maps, unifying the two phases of "seed and extend" into a single operation that executes in close to O(1) average time.

Extracting morphemes from words is a nontrivial task. Rule based stemming approaches such as Porter's algorithm have encountered some success, however they are restricted by their ability to identify a limited number of affixes and are language dependent. When dealing with languages with many affixes, rule based approaches generally require many more rules to deal with all the possible word forms. Deriving these rules requires a larger effort on the part of linguists and in some instances can be simply impractical. We propose an unsupervised ngram based approach, named Swordfish. Using ngram probabilities in the corpus, possible morphemes are identified. We look at two possible methods for identifying candidate morphemes, one using joint probabilities between two ngrams, and the second based on log odds between prefix probabilities. Initial results indicate the joint probability approach to be better for English while the prefix ratio approach is better for Finnish and Turkish.

BACKGROUND: Several ways of incorporating indels into phylogenetic analysis have been suggested. Simple indel coding has two strengths: (1) biological realism and (2) efficiency of analysis. In the method, each indel with different start and/or end positions is considered to be a separate character. The presence/absence of these indel characters is then added to the data set. ALGORITHM: We have written a program, GapCoder to automate this procedure. The program can input PIR format aligned datasets, find the indels and add the indel-based characters. The output is a NEXUS format file, which includes a table showing what region each indel characters is based on. If regions are excluded from analysis, this table makes it easy to identify the corresponding indel characters for exclusion. DISCUSSION: Manual implementation of the simple indel coding method can be very time-consuming, especially in data sets where indels are numerous and/or overlapping. GapCoder automates this method and is therefore particularly useful during procedures where phylogenetic analyses need to be repeated many times, such as when different alignments are being explored or when various taxon or character sets are being explored. GapCoder is currently available for Windows from http://www.home.duq.edu/~youngnd/GapCoder.