As discussed on Noel O'Blog's website, you can merge pdfs with the program pdftk.
For example, to merge three pdfs MolBiolCellCh1_fig1.pdf, MolBiolCellCh1_fig2.pdf and MolBiolCellCh1_fig3.pdf, you can type:
% pdftk A=MolBiolCellCh1_fig1.pdf B=MolBiolCellCh1_fig2.pdf C=MolBiolCellCh1_fig3.pdf output MolBiolCellCh1_1_figs.pdf
This makes one output pdf, MolBiolCellCh1_1_figs.pdf, that has the three other pdfs merged together in order.
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