Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple
  Sequence Alignment   Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique
in bioinformatics used to infer related residues among biological sequences.
Thus alignment accuracy is crucial to a vast range of analyses, often in ways
difficult to assess in those analyses. To compare the performance of different
aligners and help detect systematic errors in alignments, a number of
benchmarking strategies have been pursued. Here we present an overview of the
main strategies--based on simulation, consistency, protein structure, and
phylogeny--and discuss their different advantages and associated risks. We
outline a set of desirable characteristics for effective benchmarking, and
evaluate each strategy in light of them. We conclude that there is currently no
universally applicable means of benchmarking MSA, and that developers and users
of alignment tools should base their choice of benchmark depending on the
context of application--with a keen awareness of the assumptions underlying
each benchmarking strategy.

17
The categories of this paper are: q-fin
36
The categories of this paper are: cmp-lg
24
The categories of this paper are: dg-ga
14
The categories of this paper are: math-ph
32
The categories of this paper are: atom-ph
29
The categories of this paper are: funct-an
28
The categories of this paper are: alg-geom
15
The categories of this paper are: nucl-ex
27
The categories of this paper are: comp-gas
20
The categories of this paper are: acc-phys
13
The categories of this paper are: quant-ph
35
The categories of this paper are: mtrl-th
1
The categories of this paper are: cs
16
The categories of this paper are: stat
3
The categories of this paper are: physics
30
The categories of this paper are: q-alg