Any alternative to Sequencher's assembling sequence method or Dirty Data for connecting cascading sequences

Question

[Sang Chul Choi]

Hi,

I have a set of nucleotide sequences that overlap, and connect them often using a feature implemented in Sequencher that is found at http://bioinformatics.uthsc.edu/classes/module9/sequencher3.html

However, I wonder if there are alternatives to that or any free tools.

Thank you,
SangChul

[GenoMax]

Many of programs in BBMap suite accept fasta files (in addition to fastq). I am not sure if tadpole.sh would do what you are currently doing with Sequencher, but it may be worth a try. You could always convert your fasta into fake fastq files if tadpole will only take fastq.