Have the checked APC waiver programs of publishers? For example, BioMed Central has a list of countries where researchers are eligible for getting the APCs waived, though Pakistan seems not listed. And you can always contact them. PLoS ONE has a Fee Assistance programme that may help, see this example.
PeerJ is not free, but has very low costs compare to others, see here
Additionally at the moment they have a special offer to celebrate Open Access week. Until the 30th of November they will publish your paper for free if you submit it both as a preprint and as peer-reviewed. Check the details here
bioRxiv (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.
Most traditional journals (e.g. Bioinformatics for sure, BIB, NAR and JCB) do not require publishing fee as long as your paper is within the page limit, does not contain color figures and you don't choose the open access option.