Extensive answers to both of this can be found on the bowtie website: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1
How is Bowtie 2 different from Bowtie 1?
Bowtie 1 was released in 2009 and was geared toward aligning the relatively short type of sequencing reads (up to 50 bp) prevalent at the time. Since then, sequencing technology has improved both in terms of throughput (more bp produced per sequencer per day) and in terms of read length (more bp per read). Chief differences between Bowtie 1 and Bowtie 2 are:
- Bowtie 2 fully supports gapped alignment with affine gap penalties. Number of gaps and gap lengths are not restricted, except via the user-supplied scoring scheme. Bowtie 1 only finds ungapped alignments.
- For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
- Bowtie 2 supports a "local" alignment mode, which doesn't require that reads align end-to-end. This produces alignments that might be "trimmed" (or "soft clipped") at one or both extremes in a way that optimizes alignment score. Bowtie 2 also supports an "end-to-end" alignment mode which, like Bowtie 1, requires that the read align entirely.
- There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
- Bowtie 2 does away with Bowtie 1's notion of alignment "stratum". In Bowtie 2 all alignments lie along a continuous spectrum of alignment scores.
- There is no longer a distinction between "end-to-end" and "Maq-like" modes as in Bowtie 1. There is just one scoring scheme, similar to Needleman-Wunsch and Smith-Waterman.
- Bowtie 2's paired-end alignment mode is more flexible than Bowtie 1's. For example, for pairs that do not align in a paired fashion, it will attempt to find unpaired alignments for each mate.
- Bowtie 2 does not align colorspace reads.