Another Look at my old Benchmark

This is a follow-up of my previous post. Here I change the table to several charts. Hope it seems more friendly to readers. You can find the links to these libraries in that table. Their source codes, including my testing code, are available here. You may also want to see my previous posts in the [...]

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Is There an Overhead to Retrieve an Element in a Struct?

I was wondering whether retrieving an element in a struct will incur additional overhead. And so I did the following experiment. Here the same array is sorted in two ways: with or without data retrieving from a struct. Both ways yield identical results. The question is whether the compiler knows the two ways are the [...]

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Futher Discussion on Search Trees

Over the weekend, I have done a more comprehensive benchmark of various libraries on search trees. Two AVL, seven red-black tree, one Splay tree, two treap implementations are involved, together with seven hash table libraries. As I need to present a big table, I have to write it in a free-style HTML page. You can [...]

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C Array vs. C++ Vector

Here is a piece of source codes that compare C arrays and C++ vectors. It tests six scenarios: a) preallocated C array; b) dynamically growing C array; c) dynamical C vector calling kv_a macro (in my kvec.h); d) dynamical C vector calling kv_push macro (in my kvec.h); e) preallocated C++ vector and f) dynamically growing C++ [...]

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Comparison of Hash Table Libraries

As a Perl programmer, I enjoy a lot using hash tables. I keep this habit in C/C++ programming. Then what C/C++ hash libraries are available? How are they compared to each other? In this post, I will give a brief review of hash libraries and present a small benchmark showing their practical performance.
Hash table libraries
In [...]

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Comparison of Internal Sorting Algorithms

Sorting algorithm
Given an array of size N, sorting can be done in O(N log(N)) in average. The most frequently used sorting algorithms that can achieve this time complexity are quicksort, heapsort and mergesort. They usually require O(log(N)), O(1) and O(N) working space, respectively (the space complexity of mergesort can be improved at the cost of [...]

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The Best Multialignment Program?

Popular multialignment programs include: clustalw, T-coffee, dialign [PMID: 18505568, 10222408], muscle [PMID: 15318951], MAFFT [PMID: 18372315], probcons [PMID: 15687296] and probalign [PMID: 16954142]. Which is the best in practice? You can find various benchmarks in the papers listed above. I only summarize based on my understanding. It is recommended to read their papers in case [...]

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Biased Benchmarks on Short Read Aligners: ZOOM

ZOOM [PMID:18684737] is still unavailable even when the manuscript goes online. For the time being, there is no way to confirm whether their benchmarks are unbiased. Fortunately, we can collect some information from what they have presented. In the ZOOM paper, the authors give the memory consumption of ZOOM. It is 2.9GB for 12 million [...]

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