To install Linden, first you should fetch it from our git repository, or download one of the corresponding compressed zip/tar.gz packages. After downloading, change the current directory to the source directory Linden, and run make in the terminal. The linden binary will be created, which are ready to use.
git clone https://github.com/BilkentCompGen/Linden/
cd Linden
make buildIn order to make alignment between two genomes, namely genome1.fasta and genome2.fasta you need to run following commands. This command will create the file alignment.out.
$ ./linden -s1=genome1.fasta -s2=genome2.fasta > alignment.outLinden depends on the following parameters:
– block size (b): minimum size of an inner node in the ALFTree. If the size of a node is smaller than b then it is a leaf node. – chaining threshold (c): minimum number of seeds required to build a valid chain. – division length (d): approximate distance between the starting positions of two intervals in a sequence. – division window (a): number of divisions traversed in one matching step. – max indel rate (e): maximum indel rate (used as 1/e) between two link lengths, where a link length corresponds to the distance between two consecutive seeds. – k-mer size (k): length of k-mers at the starting positions of the blocks for comparisons
By default, linden uses following parameter values. a = 2 b = 2000 c = 2 d = 8000 e = 200 k = 2
In order to change the parameter values, you can use following command. For example, following command changes the value of a to 7.
$ ./linden -s1=genome1.fasta -s2=genome2.fasta -a=7 > alignment.outAnother example which sets b to 4000 and c to 5 is:
$ ./linden -s1=genome1.fasta -s2=genome2.fasta -b=4000 -c=5 > alignment.out